ascat.aspcf failed for tumor only data

[ThomasGro]

use ASCAT 2.4 without matched normal data

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

[haasek]

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.com> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4

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[ThomasGro]

Dear Kerstin,

Thank you very much for your reply.

The actual error massage was:

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample A1701-01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

What example data would you need to reproduce the error?

I have generated the input BAF and logR files with the AROMA pipeline. I have attached the first 50 rows from those files. But I can also send you R objects from the current stage of the pipeline (before the segmentation step). See the output from the R command ‘str(ascat.bc)’ and ‘str(gg)’ also attached.

I do not belief the chromosome renaming introduced new formatting. I have done this already in the past when I run the pipeline (but without the GC correction!) with Ascat2.1 and there, no problem occurred after this step. But let me know if you want to check this. So my first thought was that the GC correction step is maybe the critical one?!

Please let me know if you need any other data.

Best regards, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Montag, 18. April 2016 17:22 An: Crick-CancerGenomics/ascat ascat@noreply.github.com Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-211428702

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str(ascat.bc) List of 13 $ Tumor_LogR :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,log2ratio,total : num [1:1838128] -1.064 -0.301 0.165 -0.479 -0.725 ... ..$ A1701-02,log2ratio,total : num [1:1838128] -0.58 -0.375 -0.627 0.264 -1.456 ... ..$ A1701-03,log2ratio,total : num [1:1838128] 0.5235 -0.0274 -0.0451 -0.2053 0.1705 ... ..$ A1701-05,log2ratio,total : num [1:1838128] 0.4013 0.0851 -0.0751 0.1243 -0.1684 ... ..$ A1701-09,log2ratio,total : num [1:1838128] 0.4278 -0.1472 0.099 -0.0473 0.115 ... ..$ A1701-11,log2ratio,total : num [1:1838128] -0.6213 -0.1115 -0.1067 0.0301 0.0168 ... ..$ A1701-14,log2ratio,total : num [1:1838128] -0.73718 0.16436 -0.00593 -0.18994 -0.12872 ... ..$ A1701-16,log2ratio,total : num [1:1838128] 1.216 0.531 0.587 0.446 0.887 ... ..$ A1701-17,log2ratio,total : num [1:1838128] -0.0133 0.1652 -1.3108 -0.3043 0.318 ... ..$ A1701-18,log2ratio,total : num [1:1838128] 0.862 0.494 0.438 0.494 0.356 ... ..$ A1701-19,log2ratio,total : num [1:1838128] -0.1225 -0.0208 -0.1601 -0.2568 -0.2745 ... ..$ A1701-21,log2ratio,total : num [1:1838128] 0.675 0.1214 0.0372 0.1619 0.3637 ... ..$ A1701-22,log2ratio,total : num [1:1838128] 0.45477 -0.12108 0.00612 0.21208 -0.11725 ... ..$ A1701-26,log2ratio,total : num [1:1838128] 0.53 0.173 0.177 0.139 0.353 ... ..$ A1701-27,log2ratio,total : num [1:1838128] 0.6436 0.1175 -0.1358 0.1057 -0.0642 ... ..$ A1701-30,log2ratio,total : num [1:1838128] 0.2811 -0.143 -0.2964 -0.0682 -0.4144 ... ..$ A1801-01,log2ratio,total : num [1:1838128] -0.838 -0.022 -0.164 -0.327 -0.455 ... ..$ A1801-02,log2ratio,total : num [1:1838128] -0.3592 -0.3292 -0.4102 -0.0389 -1.3263 ... ..$ A1801-04,log2ratio,total : num [1:1838128] 0.552 0.053 0.279 -0.243 0.278 ... ..$ A1801-05,log2ratio,total : num [1:1838128] -0.3404 -0.5847 -0.51 -0.0898 -0.8582 ... ..$ A1801-06,log2ratio,total : num [1:1838128] -0.0324 -0.1867 -0.2414 -0.0411 -0.2417 ... ..$ A1801-07,log2ratio,total : num [1:1838128] -1.088 -0.58 -0.807 -0.238 -1.326 ... ..$ A1801-09,log2ratio,total : num [1:1838128] -0.0377 0.3012 0.1008 -0.1002 0.3436 ... ..$ A1801-10,log2ratio,total : num [1:1838128] 0.3937 -0.1264 -0.2854 0.0529 -0.0121 ... ..$ A1801-12,log2ratio,total : num [1:1838128] 0.2033 -0.0641 0.0946 -0.3951 0.4883 ... ..$ A1801-15,log2ratio,total : num [1:1838128] 0.2587 -0.1706 -0.0245 0.0459 -0.4473 ... ..$ A1801-17,log2ratio,total : num [1:1838128] 0.168 -0.124 0.321 -0.389 0.425 ... ..$ A1801-18,log2ratio,total : num [1:1838128] 0.637 -0.067 0.168 0.378 0.569 ... ..$ A1801-19,log2ratio,total : num [1:1838128] 0.62592 0.34983 0.47753 -0.00931 0.40493 ... ..$ A1801-20,log2ratio,total : num [1:1838128] 0.0701 0.0319 0.2329 -0.0492 0.3107 ... ..$ A1801-22,log2ratio,total : num [1:1838128] -0.247 -0.44 -0.317 0.042 -0.45 ... ..$ A1801-23,log2ratio,total : num [1:1838128] 0.1952 0.0319 -0.0321 -0.3139 0.221 ... ..$ A1801-24,log2ratio,total : num [1:1838128] 0.735 0.423 0.368 0.379 0.608 ... ..$ A1801-25,log2ratio,total : num [1:1838128] -0.3614 -0.1912 -0.3167 0.0606 -1.0455 ... ..$ A1801-27,log2ratio,total : num [1:1838128] -1.349 -0.653 -1.044 -0.462 -1.377 ... ..$ A1801-31,log2ratio,total : num [1:1838128] -0.1233 -0.4566 -0.5147 0.0551 -0.6819 ... ..$ A1801-32,log2ratio,total : num [1:1838128] -0.4494 -0.161 0.0594 -0.5185 0.0791 ... ..$ A1801-34,log2ratio,total : num [1:1838128] -0.00755 -0.07866 -0.12846 -0.22865 -0.70952 ... ..$ A1801-36,log2ratio,total : num [1:1838128] -0.208 -0.136 -0.178 -0.345 -0.859 ... ..$ A1801-38,log2ratio,total : num [1:1838128] 0.2671 0.0368 -0.09 -0.1923 0.2545 ... ..$ A1955-004,log2ratio,total : num [1:1838128] 0.0519 -0.2217 -0.094 -0.4296 -0.1114 ... ..$ A1955-006rh,log2ratio,total : num [1:1838128] -0.057 -0.0391 -0.204 -0.7818 0.0235 ... ..$ A1955-007,log2ratio,total : num [1:1838128] 0.35 -0.241 -0.296 -0.125 -0.276 ... ..$ A1955-008,log2ratio,total : num [1:1838128] 0.60433 0.00522 0.15383 -0.23609 0.52509 ... ..$ A1955-009,log2ratio,total : num [1:1838128] -0.166 -0.247 -0.23 -0.228 -0.147 ... ..$ A1955-010,log2ratio,total : num [1:1838128] -0.0902 -0.2071 -0.109 -0.5582 0.4083 ... ..$ A1955-013,log2ratio,total : num [1:1838128] -0.2269 -0.5023 -0.1698 -0.1445 -0.0886 ... ..$ A1955-014,log2ratio,total : num [1:1838128] -0.477 -0.124 -0.131 -0.355 -0.336 ... ..$ A1955-016,log2ratio,total : num [1:1838128] -0.159 -0.193 -0.137 -0.471 -0.397 ... ..$ A1955-017,log2ratio,total : num [1:1838128] 0.3317 -0.0105 -0.0246 -0.2876 0.0301 ... ..$ A1955-018,log2ratio,total : num [1:1838128] -0.08261 -0.73078 -0.63958 -0.00545 -1.62665 ... ..$ A1955-020,log2ratio,total : num [1:1838128] -0.0506 -0.2821 -0.033 -0.3097 0.013 ... ..$ A1955-021rh,log2ratio,total : num [1:1838128] 0.0403 -0.1349 0.145 -0.5794 0.3562 ... ..$ A1955-022rh,log2ratio,total : num [1:1838128] -1.332 -0.436 -0.519 -0.621 -0.536 ... ..$ A1955-033,log2ratio,total : num [1:1838128] -0.0237 -0.2418 -0.1527 -0.5331 -0.2904 ... ..$ A1955-034,log2ratio,total : num [1:1838128] 0.504 0.155 0.109 -0.3 0.56 ... ..$ A1955-035,log2ratio,total : num [1:1838128] 1.132 0.56 0.387 -0.134 0.577 ... ..$ A1955-036,log2ratio,total : num [1:1838128] -0.697 -0.823 -0.869 -0.681 -0.872 ... ..$ A1955-038,log2ratio,total : num [1:1838128] -1.957 -0.876 -1.16 -0.35 -1.543 ... ..$ A1955-039,log2ratio,total : num [1:1838128] 0.11845 -0.04037 -0.00966 -0.52031 -0.15279 ... ..$ A1955-040,log2ratio,total : num [1:1838128] -0.383 -0.525 -0.38 -0.538 -0.594 ... ..$ A1955-041,log2ratio,total : num [1:1838128] -0.19371 -0.07626 0.00504 -0.71247 -0.80625 ... ..$ A1955-045,log2ratio,total : num [1:1838128] -0.582 -0.451 -0.603 -0.965 -0.593 ... ..$ A1955-048,log2ratio,total : num [1:1838128] 0.2329 0.1001 -0.0124 -0.22 -0.084 ... ..$ A1955-049,log2ratio,total : num [1:1838128] -0.790921 -0.000494 -0.171089 -0.448867 -0.27938 ... ..$ A1955-063,log2ratio,total : num [1:1838128] 0.00685 -0.05641 0.01217 -0.08818 -0.38536 ... ..$ A1955-066,log2ratio,total : num [1:1838128] 0.21105 -0.08305 -0.00136 -0.44698 0.26788 ... ..$ A1955-067,log2ratio,total : num [1:1838128] -1.232 -0.534 -0.794 -0.636 -0.327 ... ..$ A1955-068,log2ratio,total : num [1:1838128] 0.2177 -0.0149 -0.3721 -0.3081 -0.2028 ... ..$ A1955-070,log2ratio,total : num [1:1838128] -0.208 -0.409 -0.252 -1.754 -0.6 ... ..$ A1955-072,log2ratio,total : num [1:1838128] -0.294 -0.103 -0.208 -0.187 -0.74 ... ..$ A1955-073,log2ratio,total : num [1:1838128] -0.687 -0.329 -0.467 -0.528 -1.037 ... ..$ A1955-075,log2ratio,total : num [1:1838128] -0.296 -0.252 -0.295 -0.299 -0.267 ... ..$ A1955-076,log2ratio,total : num [1:1838128] 0.628 0.142 0.317 -0.113 0.515 ... ..$ A1955-082,log2ratio,total : num [1:1838128] -0.888 -0.65 -0.344 -0.393 -0.933 ... ..$ A1955-087,log2ratio,total : num [1:1838128] -0.833 -0.718 -0.712 -0.154 -1.153 ... ..$ A1955-088,log2ratio,total : num [1:1838128] -0.947 -0.157 -0.222 0.071 -0.219 ... ..$ A1955-090,log2ratio,total : num [1:1838128] -0.166 -0.175 -0.223 -0.494 0.32 ... ..$ A1955-091,log2ratio,total : num [1:1838128] -0.8338 -0.10223 -0.17573 -0.69368 0.00222 ... ..$ A1955-092,log2ratio,total : num [1:1838128] -0.373 -0.351 -0.344 -1.336 -0.412 ... ..$ A1955-094,log2ratio,total : num [1:1838128] -1.568 -0.8 -0.955 -0.966 -1.386 ... ..$ A1955-100rh,log2ratio,total : num [1:1838128] -0.0436 -0.0108 -0.2406 -0.0861 -0.8679 ... ..$ A1955-107,log2ratio,total : num [1:1838128] -0.468 -0.625 -0.526 -0.265 -1.518 ... ..$ A1955-113,log2ratio,total : num [1:1838128] -0.38663 -0.00468 -0.22896 -0.38714 -0.13608 ... ..$ A1955-115,log2ratio,total : num [1:1838128] 0.1611 0.0217 -0.3659 -0.471 -0.3785 ... ..$ A1955-117,log2ratio,total : num [1:1838128] -1.697 -0.258 -0.523 -0.367 -2.135 ... ..$ A1955-119,log2ratio,total : num [1:1838128] 0.2656 -0.0574 -0.1316 -0.3418 0.1352 ... ..$ A1955-122,log2ratio,total : num [1:1838128] 0.0631 0.077 0.0826 -0.1981 -0.1949 ... ..$ A1955-124,log2ratio,total : num [1:1838128] -0.185 -0.34 -0.344 0.207 -0.517 ... ..$ A1955-127,log2ratio,total : num [1:1838128] -0.792 -0.638 -0.304 -0.534 -0.562 ... ..$ A1955-128,log2ratio,total : num [1:1838128] 0.121 -0.3106 -0.0577 -0.2244 -0.3533 ... ..$ A1955-130,log2ratio,total : num [1:1838128] 0.456 0.24 -0.119 -0.182 0.549 ... ..$ A1955-132,log2ratio,total : num [1:1838128] 0.0644 0.2199 -0.1128 0.1721 -0.114 ... ..$ A1955-136,log2ratio,total : num [1:1838128] 0.383 0.116 0.185 -0.541 0.281 ... ..$ A1955-138,log2ratio,total : num [1:1838128] -0.0388 -0.3934 -0.2769 -0.0267 -0.8398 ... ..$ A1955-139,log2ratio,total : num [1:1838128] 0.108 -0.103 -0.269 -0.643 -0.109 ... ..$ A1955-145,log2ratio,total : num [1:1838128] -1.1999 0.0415 0.1443 -0.3254 -1.3377 ... ..$ A1955-147,log2ratio,total : num [1:1838128] -0.702 -0.385 -0.658 -0.668 -1.333 ... ..$ AXF_984-1266,log2ratio,total : num [1:1838128] -0.269 0.587 0.574 0.249 0.46 ... .. [list output truncated] $ Tumor_BAF :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-03,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-11,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-14,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-16,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-21,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-26,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-30,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-04,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-06,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-07,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-10,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-12,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-15,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-20,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-23,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-24,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-25,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-31,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-32,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-34,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-36,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-38,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-004,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-006rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-007,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-008,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-009,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-010,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-013,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-014,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-016,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-017,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-018,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-020,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-021rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-022rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-033,fracB : num [1:1838128] NA NA NA NA NA NA NA NA 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NA NA NA NA NA NA NA NA ... ..$ A1955-113,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-115,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-117,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-119,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-122,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-124,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-127,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-128,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-130,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-132,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-136,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-138,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-139,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-145,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-147,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ AXF_984-1266,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... .. [list output truncated] $ Tumor_LogR_segmented: NULL $ Tumor_BAF_segmented : NULL $ Germline_LogR : NULL $ Germline_BAF : NULL $ SNPpos :'data.frame': 1838128 obs. of 2 variables: ..$ chromosome: int [1:1838128] 1 1 1 1 1 1 1 1 1 1 ... ..$ position : int [1:1838128] 61736 61809 61824 62153 62921 62938 72705 72777 82171 82316 ... $ ch :List of 25 ..$ : int [1:146458] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:82178] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:54181] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:9192] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chr :List of 29 ..$ : int [1:75917] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:70541] 75918 75919 75920 75921 75922 75923 75924 75925 75926 75927 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:32519] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:49659] 1008415 1008416 1008417 1008418 1008419 1008420 1008421 1008422 1008423 1008424 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:21530] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:32651] 1526934 1526935 1526936 1526937 1526938 1526939 1526940 1526941 1526942 1526943 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:8944] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:248] 1877829 1877830 1877831 1877832 1877833 1877834 1877835 1877836 1877837 1877838 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chrs : int [1:25] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ gender : chr [1:228] "XX" "XX" "XX" "XX" ... $ sexchromosomes : chr [1:2] "23" "24"

str(gg) List of 2 $ germlinegenotypes: logi [1:1838128, 1:228] NA NA NA NA NA NA ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:1838128] "CN_473963" "CN_473964" "CN_473965" "CN_477984" ... .. ..$ : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ failedarrays : NULL

name: OncotestMolecularCompendium_v1.6

tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

fullName: OncotestMolecularCompendium_v1.6,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

nbrOfFiles: 228

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MEXF_1732-7987,fracB.asb MEXF_1765-2371,fracB.asb MEXF_1792-1094,fracB.asb MEXF_1829-9933,fracB.asb MEXF_274-5165,fracB.asb MEXF_276-7909,fracB.asb MEXF_462-6609,fracB.asb MEXF_514-9135,fracB.asb MEXF_622-8283,fracB.asb MEXF_666-3786,fracB.asb MEXF_672-1172,fracB.asb MEXF_989-3233,fracB.asb OVXF_1023-5712,fracB.asb OVXF_1544-9842,fracB.asb OVXF_550-4338,fracB.asb PAXF_1657-3882,fracB.asb PAXF_1876-9329,fracB.asb PAXF_1881-8255,fracB.asb PAXF_1900-9520,fracB.asb PAXF_1965-7495,fracB.asb PAXF_1997-4821,fracB.asb PAXF_2005-5076,fracB.asb PAXF_2007-5736,fracB.asb PAXF_546-9483,fracB.asb PAXF_736-9196,fracB.asb PXF_1118-7709,fracB.asb PXF_1752-9309,fracB.asb PXF_537-1776,fracB.asb PXF_541-3557,fracB.asb PXF_698-8077,fracB.asb RXF_1003-2005,fracB.asb RXF_1183-3134,fracB.asb RXF_1220-2600,fracB.asb RXF_1393-1995,fracB.asb RXF_393-9789,fracB.asb RXF_423-8374,fracB.asb RXF_739-7683,fracB.asb SXF_117-6806,fracB.asb SXF_1186-5409,fracB.asb SXF_1301-1660,fracB.asb SXF_463-8354,fracB.asb SXF_627-8318,fracB.asb SXF_678-9969,fracB.asb TXF_593-9924,fracB.asb TXF_881-8658,fracB.asb

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names: A1701-01 A1701-02 A1701-03 A1701-05 A1701-09 A1701-11 A1701-14 A1701-16 A1701-17 A1701-18 A1701-19 A1701-21 A1701-22 A1701-26 A1701-27 A1701-30 A1801-01 A1801-02 A1801-04 A1801-05 A1801-06 A1801-07 A1801-09 A1801-10 A1801-12 A1801-15 A1801-17 A1801-18 A1801-19 A1801-20 A1801-22 A1801-23 A1801-24 A1801-25 A1801-27 A1801-31 A1801-32 A1801-34 A1801-36 A1801-38 A1955-004 A1955-006rh A1955-007 A1955-008 A1955-009 A1955-010 A1955-013 A1955-014 A1955-016 A1955-017 A1955-018 A1955-020 A1955-021rh A1955-022rh A1955-033 A1955-034 A1955-035 A1955-036 A1955-038 A1955-039 A1955-040 A1955-041 A1955-045 A1955-048 A1955-049 A1955-063 A1955-066 A1955-067 A1955-068 A1955-070 A1955-072 A1955-073 A1955-075 A1955-076 A1955-082 A1955-087 A1955-088 A1955-090 A1955-091 A1955-092 A1955-094 A1955-100rh A1955-107 A1955-113 A1955-115 A1955-117 A1955-119 A1955-122 A1955-124 A1955-127 A1955-128 A1955-130 A1955-132 A1955-136 A1955-138 A1955-139 A1955-145 A1955-147 AXF_984-1266 BXF_1258-9749 CEXF_633-6901 CNXF_498-2524 CXF_1034-4446 CXF_1086-7881 CXF_1096-1670 CXF_1103-4309 CXF_1297-3644 CXF_158-7553 CXF_1729-2517 CXF_1783-1853 CXF_1784-1174 CXF_1788-8837 CXF_2032-8080 CXF_233-2685 CXF_243-3450 CXF_260-8231 CXF_280-9681 CXF_533-7067 CXF_609-1110 CXF_676-8129 CXF_742-5370 CXF_975-3337 GXA_3002-5334 GXA_3011-8301 GXA_3013-1329 GXA_3027-4018 GXF_251-6477 GXF_281-3183 GXF_602-7914 GXF_97-9609 HNXF_536-3784 HNXF_908-7504 LXFA_1012-1139 LXFA_1041-2201 LXFA_1584-4190 LXFA_1647-3238 LXFA_1848-9907 LXFA_289-7251 LXFA_297-7167 LXFA_400-9946 LXFA_526-8219 LXFA_586-6508 LXFA_592-2222 LXFA_623-9345 LXFA_629-2652 LXFA_677-9758 LXFA_749-7793 LXFA_923-7874 LXFA_983-1825 LXFE_1022-1122 LXFE_1066-4986 LXFE_1422-8942 LXFE_211-5131 LXFE_397-1638 LXFE_409-8620 LXFE_470-6838 LXFE_597-4073 LXFE_646-7352 LXFE_690-2150 LXFE_937-5841 LXFL_1072-7634 LXFL_1121-2152 LXFL_1176-9949 LXFL_1674-2911 LXFL_430-2926 LXFL_529-6810 LXFL_625-2241 LXFS_538-3743 LXFS_573-1328 LXFS_615-5739 LXFS_650-9857 MAXF_1162-1406 MAXF_1322-1230 MAXF_1384-9459 MAXF_1398-4862 MAXF_401-9808 MAXF_449-8651 MAXF_508-1777 MAXF_574-4244 MAXF_583-3098 MAXF_857-3184 MAXF_MX1-9711 MEXF_1341-6216 MEXF_1732-7987 MEXF_1765-2371 MEXF_1792-1094 MEXF_1829-9933 MEXF_274-5165 MEXF_276-7909 MEXF_462-6609 MEXF_514-9135 MEXF_622-8283 MEXF_666-3786 MEXF_672-1172 MEXF_989-3233 OVXF_1023-5712 OVXF_1544-9842 OVXF_550-4338 PAXF_1657-3882 PAXF_1876-9329 PAXF_1881-8255 PAXF_1900-9520 PAXF_1965-7495 PAXF_1997-4821 PAXF_2005-5076 PAXF_2007-5736 PAXF_546-9483 PAXF_736-9196 PXF_1118-7709 PXF_1752-9309 PXF_537-1776 PXF_541-3557 PXF_698-8077 RXF_1003-2005 RXF_1183-3134 RXF_1220-2600 RXF_1393-1995 RXF_393-9789 RXF_423-8374 RXF_739-7683 SXF_117-6806 SXF_1186-5409 SXF_1301-1660 SXF_463-8354 SXF_627-8318 SXF_678-9969 TXF_593-9924 TXF_881-8658

tags: fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB

fullNames: A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

platform: Affymetrix

chipType: GenomeWideSNP_6,Full

nbrOfUnits: 1881415

createdOn: 2016-04-11 16:03:43 CEST

createdBy: aroma.core v3.0.0

columnTypes: character numeric numeric double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double

columnNames: unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB AFFX-5Q-123 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-456 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-789 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-ABC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A02_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A04_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A06_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A08_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A10_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

[haasek]

Dear Thomas,

could you tell me how the .LogR.PCFed.txt and .BAF.PCFed.txt files look like? These should be created before you run into the problematic line. I can’t think of a part in the GC correction that would cause this error. We are running it for quite some time now on multiple platforms. I hope the output of the segmentation files can give us more insight.

Best wishes, Kerstin

Kerstin Haase Postdoctoral Training Fellow The Francis Crick Institute Lincoln’s Inn Fields Laboratory 44 Lincoln’s Inn Fields London WC2A 3LY

T: +44 (0)20 7269 3087 E: Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.uk W: www.crick.ac.ukhttp://www.crick.ac.uk

On 19 Apr 2016, at 08:14, ThomasGro notifications@github.com<mailto:notifications@github.com> wrote:

Dear Kerstin,

Thank you very much for your reply.

The actual error massage was:

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample A1701-01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

What example data would you need to reproduce the error?

I have generated the input BAF and logR files with the AROMA pipeline. I have attached the first 50 rows from those files. But I can also send you R objects from the current stage of the pipeline (before the segmentation step). See the output from the R command ‘str(ascat.bc)’ and ‘str(gg)’ also attached.

I do not belief the chromosome renaming introduced new formatting. I have done this already in the past when I run the pipeline (but without the GC correction!) with Ascat2.1 and there, no problem occurred after this step. But let me know if you want to check this. So my first thought was that the GC correction step is maybe the critical one?!

Please let me know if you need any other data.

Best regards, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Montag, 18. April 2016 17:22 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com>> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

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str(ascat.bc) List of 13 $ Tumor_LogR :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,log2ratio,total : num [1:1838128] -1.064 -0.301 0.165 -0.479 -0.725 ... ..$ A1701-02,log2ratio,total : num [1:1838128] -0.58 -0.375 -0.627 0.264 -1.456 ... ..$ A1701-03,log2ratio,total : num [1:1838128] 0.5235 -0.0274 -0.0451 -0.2053 0.1705 ... ..$ A1701-05,log2ratio,total : num [1:1838128] 0.4013 0.0851 -0.0751 0.1243 -0.1684 ... ..$ A1701-09,log2ratio,total : num [1:1838128] 0.4278 -0.1472 0.099 -0.0473 0.115 ... ..$ A1701-11,log2ratio,total : num [1:1838128] -0.6213 -0.1115 -0.1067 0.0301 0.0168 ... ..$ A1701-14,log2ratio,total : num [1:1838128] -0.73718 0.16436 -0.00593 -0.18994 -0.12872 ... ..$ A1701-16,log2ratio,total : num [1:1838128] 1.216 0.531 0.587 0.446 0.887 ... ..$ A1701-17,log2ratio,total : num [1:1838128] -0.0133 0.1652 -1.3108 -0.3043 0.318 ... ..$ A1701-18,log2ratio,total : num [1:1838128] 0.862 0.494 0.438 0.494 0.356 ... ..$ A1701-19,log2ratio,total : num [1:1838128] -0.1225 -0.0208 -0.1601 -0.2568 -0.2745 ... ..$ A1701-21,log2ratio,total : num [1:1838128] 0.675 0.1214 0.0372 0.1619 0.3637 ... ..$ A1701-22,log2ratio,total : num [1:1838128] 0.45477 -0.12108 0.00612 0.21208 -0.11725 ... ..$ A1701-26,log2ratio,total : num [1:1838128] 0.53 0.173 0.177 0.139 0.353 ... ..$ A1701-27,log2ratio,total : num [1:1838128] 0.6436 0.1175 -0.1358 0.1057 -0.0642 ... ..$ A1701-30,log2ratio,total : num [1:1838128] 0.2811 -0.143 -0.2964 -0.0682 -0.4144 ... ..$ A1801-01,log2ratio,total : num [1:1838128] -0.838 -0.022 -0.164 -0.327 -0.455 ... ..$ A1801-02,log2ratio,total : num [1:1838128] -0.3592 -0.3292 -0.4102 -0.0389 -1.3263 ... ..$ A1801-04,log2ratio,total : num [1:1838128] 0.552 0.053 0.279 -0.243 0.278 ... ..$ A1801-05,log2ratio,total : num [1:1838128] -0.3404 -0.5847 -0.51 -0.0898 -0.8582 ... ..$ A1801-06,log2ratio,total : num [1:1838128] -0.0324 -0.1867 -0.2414 -0.0411 -0.2417 ... ..$ A1801-07,log2ratio,total : num [1:1838128] -1.088 -0.58 -0.807 -0.238 -1.326 ... ..$ A1801-09,log2ratio,total : num [1:1838128] -0.0377 0.3012 0.1008 -0.1002 0.3436 ... ..$ A1801-10,log2ratio,total : num [1:1838128] 0.3937 -0.1264 -0.2854 0.0529 -0.0121 ... ..$ A1801-12,log2ratio,total : num [1:1838128] 0.2033 -0.0641 0.0946 -0.3951 0.4883 ... ..$ A1801-15,log2ratio,total : num [1:1838128] 0.2587 -0.1706 -0.0245 0.0459 -0.4473 ... ..$ A1801-17,log2ratio,total : num [1:1838128] 0.168 -0.124 0.321 -0.389 0.425 ... ..$ A1801-18,log2ratio,total : num [1:1838128] 0.637 -0.067 0.168 0.378 0.569 ... ..$ A1801-19,log2ratio,total : num [1:1838128] 0.62592 0.34983 0.47753 -0.00931 0.40493 ... ..$ A1801-20,log2ratio,total : num [1:1838128] 0.0701 0.0319 0.2329 -0.0492 0.3107 ... ..$ A1801-22,log2ratio,total : num [1:1838128] -0.247 -0.44 -0.317 0.042 -0.45 ... ..$ A1801-23,log2ratio,total : num [1:1838128] 0.1952 0.0319 -0.0321 -0.3139 0.221 ... ..$ A1801-24,log2ratio,total : num [1:1838128] 0.735 0.423 0.368 0.379 0.608 ... ..$ A1801-25,log2ratio,total : num [1:1838128] -0.3614 -0.1912 -0.3167 0.0606 -1.0455 ... ..$ A1801-27,log2ratio,total : num [1:1838128] -1.349 -0.653 -1.044 -0.462 -1.377 ... ..$ A1801-31,log2ratio,total : num [1:1838128] -0.1233 -0.4566 -0.5147 0.0551 -0.6819 ... ..$ A1801-32,log2ratio,total : num [1:1838128] -0.4494 -0.161 0.0594 -0.5185 0.0791 ... ..$ A1801-34,log2ratio,total : num [1:1838128] -0.00755 -0.07866 -0.12846 -0.22865 -0.70952 ... ..$ A1801-36,log2ratio,total : num [1:1838128] -0.208 -0.136 -0.178 -0.345 -0.859 ... ..$ A1801-38,log2ratio,total : num [1:1838128] 0.2671 0.0368 -0.09 -0.1923 0.2545 ... ..$ A1955-004,log2ratio,total : num [1:1838128] 0.0519 -0.2217 -0.094 -0.4296 -0.1114 ... ..$ A1955-006rh,log2ratio,total : num [1:1838128] -0.057 -0.0391 -0.204 -0.7818 0.0235 ... ..$ A1955-007,log2ratio,total : num [1:1838128] 0.35 -0.241 -0.296 -0.125 -0.276 ... ..$ A1955-008,log2ratio,total : num [1:1838128] 0.60433 0.00522 0.15383 -0.23609 0.52509 ... ..$ A1955-009,log2ratio,total : num [1:1838128] -0.166 -0.247 -0.23 -0.228 -0.147 ... ..$ A1955-010,log2ratio,total : num [1:1838128] -0.0902 -0.2071 -0.109 -0.5582 0.4083 ... ..$ A1955-013,log2ratio,total : num [1:1838128] -0.2269 -0.5023 -0.1698 -0.1445 -0.0886 ... ..$ A1955-014,log2ratio,total : num [1:1838128] -0.477 -0.124 -0.131 -0.355 -0.336 ... ..$ A1955-016,log2ratio,total : num [1:1838128] -0.159 -0.193 -0.137 -0.471 -0.397 ... ..$ A1955-017,log2ratio,total : num [1:1838128] 0.3317 -0.0105 -0.0246 -0.2876 0.0301 ... ..$ A1955-018,log2ratio,total : num [1:1838128] -0.08261 -0.73078 -0.63958 -0.00545 -1.62665 ... ..$ A1955-020,log2ratio,total : num [1:1838128] -0.0506 -0.2821 -0.033 -0.3097 0.013 ... ..$ A1955-021rh,log2ratio,total : num [1:1838128] 0.0403 -0.1349 0.145 -0.5794 0.3562 ... ..$ A1955-022rh,log2ratio,total : num [1:1838128] -1.332 -0.436 -0.519 -0.621 -0.536 ... ..$ A1955-033,log2ratio,total : num [1:1838128] -0.0237 -0.2418 -0.1527 -0.5331 -0.2904 ... ..$ A1955-034,log2ratio,total : num [1:1838128] 0.504 0.155 0.109 -0.3 0.56 ... ..$ A1955-035,log2ratio,total : num [1:1838128] 1.132 0.56 0.387 -0.134 0.577 ... ..$ A1955-036,log2ratio,total : num [1:1838128] -0.697 -0.823 -0.869 -0.681 -0.872 ... ..$ A1955-038,log2ratio,total : num [1:1838128] -1.957 -0.876 -1.16 -0.35 -1.543 ... ..$ A1955-039,log2ratio,total : num [1:1838128] 0.11845 -0.04037 -0.00966 -0.52031 -0.15279 ... ..$ A1955-040,log2ratio,total : num [1:1838128] -0.383 -0.525 -0.38 -0.538 -0.594 ... ..$ A1955-041,log2ratio,total : num [1:1838128] -0.19371 -0.07626 0.00504 -0.71247 -0.80625 ... ..$ A1955-045,log2ratio,total : num [1:1838128] -0.582 -0.451 -0.603 -0.965 -0.593 ... ..$ A1955-048,log2ratio,total : num [1:1838128] 0.2329 0.1001 -0.0124 -0.22 -0.084 ... ..$ A1955-049,log2ratio,total : num [1:1838128] -0.790921 -0.000494 -0.171089 -0.448867 -0.27938 ... ..$ A1955-063,log2ratio,total : num [1:1838128] 0.00685 -0.05641 0.01217 -0.08818 -0.38536 ... ..$ A1955-066,log2ratio,total : num [1:1838128] 0.21105 -0.08305 -0.00136 -0.44698 0.26788 ... ..$ A1955-067,log2ratio,total : num [1:1838128] -1.232 -0.534 -0.794 -0.636 -0.327 ... ..$ A1955-068,log2ratio,total : num [1:1838128] 0.2177 -0.0149 -0.3721 -0.3081 -0.2028 ... ..$ A1955-070,log2ratio,total : num [1:1838128] -0.208 -0.409 -0.252 -1.754 -0.6 ... ..$ A1955-072,log2ratio,total : num [1:1838128] -0.294 -0.103 -0.208 -0.187 -0.74 ... ..$ A1955-073,log2ratio,total : num [1:1838128] -0.687 -0.329 -0.467 -0.528 -1.037 ... ..$ A1955-075,log2ratio,total : num [1:1838128] -0.296 -0.252 -0.295 -0.299 -0.267 ... ..$ A1955-076,log2ratio,total : num [1:1838128] 0.628 0.142 0.317 -0.113 0.515 ... ..$ A1955-082,log2ratio,total : num [1:1838128] -0.888 -0.65 -0.344 -0.393 -0.933 ... ..$ A1955-087,log2ratio,total : num [1:1838128] -0.833 -0.718 -0.712 -0.154 -1.153 ... ..$ A1955-088,log2ratio,total : num [1:1838128] -0.947 -0.157 -0.222 0.071 -0.219 ... ..$ A1955-090,log2ratio,total : num [1:1838128] -0.166 -0.175 -0.223 -0.494 0.32 ... ..$ A1955-091,log2ratio,total : num [1:1838128] -0.8338 -0.10223 -0.17573 -0.69368 0.00222 ... ..$ A1955-092,log2ratio,total : num [1:1838128] -0.373 -0.351 -0.344 -1.336 -0.412 ... ..$ A1955-094,log2ratio,total : num [1:1838128] -1.568 -0.8 -0.955 -0.966 -1.386 ... ..$ A1955-100rh,log2ratio,total : num [1:1838128] -0.0436 -0.0108 -0.2406 -0.0861 -0.8679 ... ..$ A1955-107,log2ratio,total : num [1:1838128] -0.468 -0.625 -0.526 -0.265 -1.518 ... ..$ A1955-113,log2ratio,total : num [1:1838128] -0.38663 -0.00468 -0.22896 -0.38714 -0.13608 ... ..$ A1955-115,log2ratio,total : num [1:1838128] 0.1611 0.0217 -0.3659 -0.471 -0.3785 ... ..$ A1955-117,log2ratio,total : num [1:1838128] -1.697 -0.258 -0.523 -0.367 -2.135 ... ..$ A1955-119,log2ratio,total : num [1:1838128] 0.2656 -0.0574 -0.1316 -0.3418 0.1352 ... ..$ A1955-122,log2ratio,total : num [1:1838128] 0.0631 0.077 0.0826 -0.1981 -0.1949 ... ..$ A1955-124,log2ratio,total : num [1:1838128] -0.185 -0.34 -0.344 0.207 -0.517 ... ..$ A1955-127,log2ratio,total : num [1:1838128] -0.792 -0.638 -0.304 -0.534 -0.562 ... ..$ A1955-128,log2ratio,total : num [1:1838128] 0.121 -0.3106 -0.0577 -0.2244 -0.3533 ... ..$ A1955-130,log2ratio,total : num [1:1838128] 0.456 0.24 -0.119 -0.182 0.549 ... ..$ A1955-132,log2ratio,total : num [1:1838128] 0.0644 0.2199 -0.1128 0.1721 -0.114 ... ..$ A1955-136,log2ratio,total : num [1:1838128] 0.383 0.116 0.185 -0.541 0.281 ... ..$ A1955-138,log2ratio,total : num [1:1838128] -0.0388 -0.3934 -0.2769 -0.0267 -0.8398 ... ..$ A1955-139,log2ratio,total : num [1:1838128] 0.108 -0.103 -0.269 -0.643 -0.109 ... ..$ A1955-145,log2ratio,total : num [1:1838128] -1.1999 0.0415 0.1443 -0.3254 -1.3377 ... ..$ A1955-147,log2ratio,total : num [1:1838128] -0.702 -0.385 -0.658 -0.668 -1.333 ... ..$ AXF_984-1266,log2ratio,total : num [1:1838128] -0.269 0.587 0.574 0.249 0.46 ... .. [list output truncated] $ Tumor_BAF :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-03,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-11,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-14,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-16,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-21,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-26,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-30,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-04,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-06,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-07,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-10,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-12,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-15,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-20,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-23,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-24,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-25,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-31,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-32,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-34,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-36,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-38,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-004,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-006rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-007,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-008,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-009,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-010,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-013,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-014,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-016,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-017,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-018,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-020,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-021rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-022rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-033,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-034,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-035,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-036,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-038,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-039,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-040,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-041,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-045,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-048,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-049,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-063,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-066,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-067,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-068,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-070,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-072,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-073,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-075,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-076,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-082,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-087,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-088,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-090,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-091,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-092,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-094,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-100rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-107,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-113,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-115,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-117,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-119,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-122,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-124,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-127,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-128,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-130,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-132,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-136,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-138,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-139,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-145,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-147,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ AXF_984-1266,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... .. [list output truncated] $ Tumor_LogR_segmented: NULL $ Tumor_BAF_segmented : NULL $ Germline_LogR : NULL $ Germline_BAF : NULL $ SNPpos :'data.frame': 1838128 obs. of 2 variables: ..$ chromosome: int [1:1838128] 1 1 1 1 1 1 1 1 1 1 ... ..$ position : int [1:1838128] 61736 61809 61824 62153 62921 62938 72705 72777 82171 82316 ... $ ch :List of 25 ..$ : int [1:146458] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:82178] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:54181] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:9192] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chr :List of 29 ..$ : int [1:75917] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:70541] 75918 75919 75920 75921 75922 75923 75924 75925 75926 75927 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:32519] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:49659] 1008415 1008416 1008417 1008418 1008419 1008420 1008421 1008422 1008423 1008424 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:21530] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:32651] 1526934 1526935 1526936 1526937 1526938 1526939 1526940 1526941 1526942 1526943 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:8944] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:248] 1877829 1877830 1877831 1877832 1877833 1877834 1877835 1877836 1877837 1877838 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chrs : int [1:25] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ gender : chr [1:228] "XX" "XX" "XX" "XX" ... $ sexchromosomes : chr [1:2] "23" "24"

str(gg) List of 2 $ germlinegenotypes: logi [1:1838128, 1:228] NA NA NA NA NA NA ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:1838128] "CN_473963" "CN_473964" "CN_473965" "CN_477984" ... .. ..$ : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ failedarrays : NULL

name: OncotestMolecularCompendium_v1.6

tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

fullName: OncotestMolecularCompendium_v1.6,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

nbrOfFiles: 228

srcFiles: A1701-01,fracB.asb A1701-02,fracB.asb A1701-03,fracB.asb A1701-05,fracB.asb A1701-09,fracB.asb A1701-11,fracB.asb A1701-14,fracB.asb A1701-16,fracB.asb A1701-17,fracB.asb A1701-18,fracB.asb A1701-19,fracB.asb A1701-21,fracB.asb A1701-22,fracB.asb A1701-26,fracB.asb A1701-27,fracB.asb A1701-30,fracB.asb A1801-01,fracB.asb A1801-02,fracB.asb A1801-04,fracB.asb A1801-05,fracB.asb A1801-06,fracB.asb A1801-07,fracB.asb A1801-09,fracB.asb A1801-10,fracB.asb A1801-12,fracB.asb A1801-15,fracB.asb A1801-17,fracB.asb A1801-18,fracB.asb A1801-19,fracB.asb A1801-20,fracB.asb A1801-22,fracB.asb A1801-23,fracB.asb A1801-24,fracB.asb A1801-25,fracB.asb A1801-27,fracB.asb A1801-31,fracB.asb A1801-32,fracB.asb A1801-34,fracB.asb A1801-36,fracB.asb A1801-38,fracB.asb A1955-004,fracB.asb A1955-006rh,fracB.asb A1955-007,fracB.asb A1955-008,fracB.asb A1955-009,fracB.asb A1955-010,fracB.asb A1955-013,fracB.asb A1955-014,fracB.asb A1955-016,fracB.asb A1955-017,fracB.asb A1955-018,fracB.asb A1955-020,fracB.asb A1955-021rh,fracB.asb A1955-022rh,fracB.asb A1955-033,fracB.asb A1955-034,fracB.asb A1955-035,fracB.asb A1955-036,fracB.asb A1955-038,fracB.asb A1955-039,fracB.asb A1955-040,fracB.asb A1955-041,fracB.asb A1955-045,fracB.asb A1955-048,fracB.asb A1955-049,fracB.asb A1955-063,fracB.asb A1955-066,fracB.asb A1955-067,fracB.asb A1955-068,fracB.asb A1955-070,fracB.asb A1955-072,fracB.asb A1955-073,fracB.asb A1955-075,fracB.asb A1955-076,fracB.asb A1955-082,fracB.asb A1955-087,fracB.asb A1955-088,fracB.asb A1955-090,fracB.asb A1955-091,fracB.asb A1955-092,fracB.asb A1955-094,fracB.asb A1955-100rh,fracB.asb A1955-107,fracB.asb A1955-113,fracB.asb A1955-115,fracB.asb A1955-117,fracB.asb A1955-119,fracB.asb A1955-122,fracB.asb A1955-124,fracB.asb A1955-127,fracB.asb A1955-128,fracB.asb A1955-130,fracB.asb A1955-132,fracB.asb A1955-136,fracB.asb A1955-138,fracB.asb A1955-139,fracB.asb A1955-145,fracB.asb A1955-147,fracB.asb AXF_984-1266,fracB.asb BXF_1258-9749,fracB.asb CEXF_633-6901,fracB.asb CNXF_498-2524,fracB.asb CXF_1034-4446,fracB.asb CXF_1086-7881,fracB.asb CXF_1096-1670,fracB.asb CXF_1103-4309,fracB.asb CXF_1297-3644,fracB.asb CXF_158-7553,fracB.asb CXF_1729-2517,fracB.asb CXF_1783-1853,fracB.asb CXF_1784-1174,fracB.asb CXF_1788-8837,fracB.asb CXF_2032-8080,fracB.asb CXF_233-2685,fracB.asb CXF_243-3450,fracB.asb CXF_260-8231,fracB.asb CXF_280-9681,fracB.asb CXF_533-7067,fracB.asb CXF_609-1110,fracB.asb CXF_676-8129,fracB.asb CXF_742-5370,fracB.asb CXF_975-3337,fracB.asb GXA_3002-5334,fracB.asb GXA_3011-8301,fracB.asb GXA_3013-1329,fracB.asb GXA_3027-4018,fracB.asb GXF_251-6477,fracB.asb GXF_281-3183,fracB.asb GXF_602-7914,fracB.asb GXF_97-9609,fracB.asb HNXF_536-3784,fracB.asb HNXF_908-7504,fracB.asb LXFA_1012-1139,fracB.asb LXFA_1041-2201,fracB.asb LXFA_1584-4190,fracB.asb LXFA_1647-3238,fracB.asb LXFA_1848-9907,fracB.asb LXFA_289-7251,fracB.asb LXFA_297-7167,fracB.asb LXFA_400-9946,fracB.asb LXFA_526-8219,fracB.asb LXFA_586-6508,fracB.asb LXFA_592-2222,fracB.asb LXFA_623-9345,fracB.asb LXFA_629-2652,fracB.asb LXFA_677-9758,fracB.asb LXFA_749-7793,fracB.asb LXFA_923-7874,fracB.asb LXFA_983-1825,fracB.asb LXFE_1022-1122,fracB.asb LXFE_1066-4986,fracB.asb LXFE_1422-8942,fracB.asb LXFE_211-5131,fracB.asb LXFE_397-1638,fracB.asb LXFE_409-8620,fracB.asb LXFE_470-6838,fracB.asb LXFE_597-4073,fracB.asb LXFE_646-7352,fracB.asb LXFE_690-2150,fracB.asb LXFE_937-5841,fracB.asb LXFL_1072-7634,fracB.asb LXFL_1121-2152,fracB.asb LXFL_1176-9949,fracB.asb LXFL_1674-2911,fracB.asb LXFL_430-2926,fracB.asb LXFL_529-6810,fracB.asb LXFL_625-2241,fracB.asb LXFS_538-3743,fracB.asb LXFS_573-1328,fracB.asb LXFS_615-5739,fracB.asb LXFS_650-9857,fracB.asb MAXF_1162-1406,fracB.asb MAXF_1322-1230,fracB.asb MAXF_1384-9459,fracB.asb MAXF_1398-4862,fracB.asb MAXF_401-9808,fracB.asb MAXF_449-8651,fracB.asb MAXF_508-1777,fracB.asb MAXF_574-4244,fracB.asb MAXF_583-3098,fracB.asb MAXF_857-3184,fracB.asb MAXF_MX1-9711,fracB.asb MEXF_1341-6216,fracB.asb MEXF_1732-7987,fracB.asb MEXF_1765-2371,fracB.asb MEXF_1792-1094,fracB.asb MEXF_1829-9933,fracB.asb MEXF_274-5165,fracB.asb MEXF_276-7909,fracB.asb MEXF_462-6609,fracB.asb MEXF_514-9135,fracB.asb MEXF_622-8283,fracB.asb MEXF_666-3786,fracB.asb MEXF_672-1172,fracB.asb MEXF_989-3233,fracB.asb OVXF_1023-5712,fracB.asb OVXF_1544-9842,fracB.asb OVXF_550-4338,fracB.asb PAXF_1657-3882,fracB.asb PAXF_1876-9329,fracB.asb PAXF_1881-8255,fracB.asb PAXF_1900-9520,fracB.asb PAXF_1965-7495,fracB.asb PAXF_1997-4821,fracB.asb PAXF_2005-5076,fracB.asb PAXF_2007-5736,fracB.asb PAXF_546-9483,fracB.asb PAXF_736-9196,fracB.asb PXF_1118-7709,fracB.asb PXF_1752-9309,fracB.asb PXF_537-1776,fracB.asb PXF_541-3557,fracB.asb PXF_698-8077,fracB.asb RXF_1003-2005,fracB.asb RXF_1183-3134,fracB.asb RXF_1220-2600,fracB.asb RXF_1393-1995,fracB.asb RXF_393-9789,fracB.asb RXF_423-8374,fracB.asb RXF_739-7683,fracB.asb SXF_117-6806,fracB.asb SXF_1186-5409,fracB.asb SXF_1301-1660,fracB.asb SXF_463-8354,fracB.asb SXF_627-8318,fracB.asb SXF_678-9969,fracB.asb TXF_593-9924,fracB.asb TXF_881-8658,fracB.asb

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names: A1701-01 A1701-02 A1701-03 A1701-05 A1701-09 A1701-11 A1701-14 A1701-16 A1701-17 A1701-18 A1701-19 A1701-21 A1701-22 A1701-26 A1701-27 A1701-30 A1801-01 A1801-02 A1801-04 A1801-05 A1801-06 A1801-07 A1801-09 A1801-10 A1801-12 A1801-15 A1801-17 A1801-18 A1801-19 A1801-20 A1801-22 A1801-23 A1801-24 A1801-25 A1801-27 A1801-31 A1801-32 A1801-34 A1801-36 A1801-38 A1955-004 A1955-006rh A1955-007 A1955-008 A1955-009 A1955-010 A1955-013 A1955-014 A1955-016 A1955-017 A1955-018 A1955-020 A1955-021rh A1955-022rh A1955-033 A1955-034 A1955-035 A1955-036 A1955-038 A1955-039 A1955-040 A1955-041 A1955-045 A1955-048 A1955-049 A1955-063 A1955-066 A1955-067 A1955-068 A1955-070 A1955-072 A1955-073 A1955-075 A1955-076 A1955-082 A1955-087 A1955-088 A1955-090 A1955-091 A1955-092 A1955-094 A1955-100rh A1955-107 A1955-113 A1955-115 A1955-117 A1955-119 A1955-122 A1955-124 A1955-127 A1955-128 A1955-130 A1955-132 A1955-136 A1955-138 A1955-139 A1955-145 A1955-147 AXF_984-1266 BXF_1258-9749 CEXF_633-6901 CNXF_498-2524 CXF_1034-4446 CXF_1086-7881 CXF_1096-1670 CXF_1103-4309 CXF_1297-3644 CXF_158-7553 CXF_1729-2517 CXF_1783-1853 CXF_1784-1174 CXF_1788-8837 CXF_2032-8080 CXF_233-2685 CXF_243-3450 CXF_260-8231 CXF_280-9681 CXF_533-7067 CXF_609-1110 CXF_676-8129 CXF_742-5370 CXF_975-3337 GXA_3002-5334 GXA_3011-8301 GXA_3013-1329 GXA_3027-4018 GXF_251-6477 GXF_281-3183 GXF_602-7914 GXF_97-9609 HNXF_536-3784 HNXF_908-7504 LXFA_1012-1139 LXFA_1041-2201 LXFA_1584-4190 LXFA_1647-3238 LXFA_1848-9907 LXFA_289-7251 LXFA_297-7167 LXFA_400-9946 LXFA_526-8219 LXFA_586-6508 LXFA_592-2222 LXFA_623-9345 LXFA_629-2652 LXFA_677-9758 LXFA_749-7793 LXFA_923-7874 LXFA_983-1825 LXFE_1022-1122 LXFE_1066-4986 LXFE_1422-8942 LXFE_211-5131 LXFE_397-1638 LXFE_409-8620 LXFE_470-6838 LXFE_597-4073 LXFE_646-7352 LXFE_690-2150 LXFE_937-5841 LXFL_1072-7634 LXFL_1121-2152 LXFL_1176-9949 LXFL_1674-2911 LXFL_430-2926 LXFL_529-6810 LXFL_625-2241 LXFS_538-3743 LXFS_573-1328 LXFS_615-5739 LXFS_650-9857 MAXF_1162-1406 MAXF_1322-1230 MAXF_1384-9459 MAXF_1398-4862 MAXF_401-9808 MAXF_449-8651 MAXF_508-1777 MAXF_574-4244 MAXF_583-3098 MAXF_857-3184 MAXF_MX1-9711 MEXF_1341-6216 MEXF_1732-7987 MEXF_1765-2371 MEXF_1792-1094 MEXF_1829-9933 MEXF_274-5165 MEXF_276-7909 MEXF_462-6609 MEXF_514-9135 MEXF_622-8283 MEXF_666-3786 MEXF_672-1172 MEXF_989-3233 OVXF_1023-5712 OVXF_1544-9842 OVXF_550-4338 PAXF_1657-3882 PAXF_1876-9329 PAXF_1881-8255 PAXF_1900-9520 PAXF_1965-7495 PAXF_1997-4821 PAXF_2005-5076 PAXF_2007-5736 PAXF_546-9483 PAXF_736-9196 PXF_1118-7709 PXF_1752-9309 PXF_537-1776 PXF_541-3557 PXF_698-8077 RXF_1003-2005 RXF_1183-3134 RXF_1220-2600 RXF_1393-1995 RXF_393-9789 RXF_423-8374 RXF_739-7683 SXF_117-6806 SXF_1186-5409 SXF_1301-1660 SXF_463-8354 SXF_627-8318 SXF_678-9969 TXF_593-9924 TXF_881-8658

tags: fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB

fullNames: A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

platform: Affymetrix

chipType: GenomeWideSNP_6,Full

nbrOfUnits: 1881415

createdOn: 2016-04-11 16:03:43 CEST

createdBy: aroma.core v3.0.0

columnTypes: character numeric numeric double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double

columnNames: unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB AFFX-5Q-123 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-456 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-789 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-ABC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A02_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A04_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A06_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A08_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A10_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

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[ThomasGro]

Dear Kerstin, thank you for your efforts. I have attached the bzip2 compressed files. Best regards, Thomas

Von: haasek [mailto:notifications@github.com] Gesendet: Dienstag, 19. April 2016 13:47 An: Crick-CancerGenomics/ascat ascat@noreply.github.com Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you tell me how the .LogR.PCFed.txt and .BAF.PCFed.txt files look like? These should be created before you run into the problematic line. I can’t think of a part in the GC correction that would cause this error. We are running it for quite some time now on multiple platforms. I hope the output of the segmentation files can give us more insight.

Best wishes, Kerstin

Kerstin Haase Postdoctoral Training Fellow The Francis Crick Institute Lincoln’s Inn Fields Laboratory 44 Lincoln’s Inn Fields London WC2A 3LY

T: +44 (0)20 7269 3087 E: Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk W: www.crick.ac.ukhttp://www.crick.ac.ukhttp://www.crick.ac.uk%3chttp:/www.crick.ac.uk

On 19 Apr 2016, at 08:14, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

Dear Kerstin,

Thank you very much for your reply.

The actual error massage was:

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample A1701-01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

What example data would you need to reproduce the error?

I have generated the input BAF and logR files with the AROMA pipeline. I have attached the first 50 rows from those files. But I can also send you R objects from the current stage of the pipeline (before the segmentation step). See the output from the R command ‘str(ascat.bc)’ and ‘str(gg)’ also attached.

I do not belief the chromosome renaming introduced new formatting. I have done this already in the past when I run the pipeline (but without the GC correction!) with Ascat2.1 and there, no problem occurred after this step. But let me know if you want to check this. So my first thought was that the GC correction step is maybe the critical one?!

Please let me know if you need any other data.

Best regards, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Montag, 18. April 2016 17:22 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com<mailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com>>> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

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str(ascat.bc) List of 13 $ Tumor_LogR :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,log2ratio,total : num [1:1838128] -1.064 -0.301 0.165 -0.479 -0.725 ... ..$ A1701-02,log2ratio,total : num [1:1838128] -0.58 -0.375 -0.627 0.264 -1.456 ... ..$ A1701-03,log2ratio,total : num [1:1838128] 0.5235 -0.0274 -0.0451 -0.2053 0.1705 ... ..$ A1701-05,log2ratio,total : num [1:1838128] 0.4013 0.0851 -0.0751 0.1243 -0.1684 ... ..$ A1701-09,log2ratio,total : num [1:1838128] 0.4278 -0.1472 0.099 -0.0473 0.115 ... ..$ A1701-11,log2ratio,total : num [1:1838128] -0.6213 -0.1115 -0.1067 0.0301 0.0168 ... ..$ A1701-14,log2ratio,total : num [1:1838128] -0.73718 0.16436 -0.00593 -0.18994 -0.12872 ... ..$ A1701-16,log2ratio,total : num [1:1838128] 1.216 0.531 0.587 0.446 0.887 ... ..$ A1701-17,log2ratio,total : num [1:1838128] -0.0133 0.1652 -1.3108 -0.3043 0.318 ... ..$ A1701-18,log2ratio,total : num [1:1838128] 0.862 0.494 0.438 0.494 0.356 ... ..$ A1701-19,log2ratio,total : num [1:1838128] -0.1225 -0.0208 -0.1601 -0.2568 -0.2745 ... ..$ A1701-21,log2ratio,total : num [1:1838128] 0.675 0.1214 0.0372 0.1619 0.3637 ... ..$ A1701-22,log2ratio,total : num [1:1838128] 0.45477 -0.12108 0.00612 0.21208 -0.11725 ... ..$ A1701-26,log2ratio,total : num [1:1838128] 0.53 0.173 0.177 0.139 0.353 ... ..$ A1701-27,log2ratio,total : num [1:1838128] 0.6436 0.1175 -0.1358 0.1057 -0.0642 ... ..$ A1701-30,log2ratio,total : num [1:1838128] 0.2811 -0.143 -0.2964 -0.0682 -0.4144 ... ..$ A1801-01,log2ratio,total : num [1:1838128] -0.838 -0.022 -0.164 -0.327 -0.455 ... ..$ A1801-02,log2ratio,total : num [1:1838128] -0.3592 -0.3292 -0.4102 -0.0389 -1.3263 ... ..$ A1801-04,log2ratio,total : num [1:1838128] 0.552 0.053 0.279 -0.243 0.278 ... ..$ A1801-05,log2ratio,total : num [1:1838128] -0.3404 -0.5847 -0.51 -0.0898 -0.8582 ... ..$ A1801-06,log2ratio,total : num [1:1838128] -0.0324 -0.1867 -0.2414 -0.0411 -0.2417 ... ..$ A1801-07,log2ratio,total : num [1:1838128] -1.088 -0.58 -0.807 -0.238 -1.326 ... ..$ A1801-09,log2ratio,total : num [1:1838128] -0.0377 0.3012 0.1008 -0.1002 0.3436 ... ..$ A1801-10,log2ratio,total : num [1:1838128] 0.3937 -0.1264 -0.2854 0.0529 -0.0121 ... ..$ A1801-12,log2ratio,total : num [1:1838128] 0.2033 -0.0641 0.0946 -0.3951 0.4883 ... ..$ A1801-15,log2ratio,total : num [1:1838128] 0.2587 -0.1706 -0.0245 0.0459 -0.4473 ... ..$ A1801-17,log2ratio,total : num [1:1838128] 0.168 -0.124 0.321 -0.389 0.425 ... ..$ A1801-18,log2ratio,total : num [1:1838128] 0.637 -0.067 0.168 0.378 0.569 ... ..$ A1801-19,log2ratio,total : num [1:1838128] 0.62592 0.34983 0.47753 -0.00931 0.40493 ... ..$ A1801-20,log2ratio,total : num [1:1838128] 0.0701 0.0319 0.2329 -0.0492 0.3107 ... ..$ A1801-22,log2ratio,total : num [1:1838128] -0.247 -0.44 -0.317 0.042 -0.45 ... ..$ A1801-23,log2ratio,total : num [1:1838128] 0.1952 0.0319 -0.0321 -0.3139 0.221 ... ..$ A1801-24,log2ratio,total : num [1:1838128] 0.735 0.423 0.368 0.379 0.608 ... ..$ A1801-25,log2ratio,total : num [1:1838128] -0.3614 -0.1912 -0.3167 0.0606 -1.0455 ... ..$ A1801-27,log2ratio,total : num [1:1838128] -1.349 -0.653 -1.044 -0.462 -1.377 ... ..$ A1801-31,log2ratio,total : num [1:1838128] -0.1233 -0.4566 -0.5147 0.0551 -0.6819 ... ..$ A1801-32,log2ratio,total : num [1:1838128] -0.4494 -0.161 0.0594 -0.5185 0.0791 ... ..$ A1801-34,log2ratio,total : num [1:1838128] -0.00755 -0.07866 -0.12846 -0.22865 -0.70952 ... ..$ A1801-36,log2ratio,total : num [1:1838128] -0.208 -0.136 -0.178 -0.345 -0.859 ... ..$ A1801-38,log2ratio,total : num [1:1838128] 0.2671 0.0368 -0.09 -0.1923 0.2545 ... ..$ A1955-004,log2ratio,total : num [1:1838128] 0.0519 -0.2217 -0.094 -0.4296 -0.1114 ... ..$ A1955-006rh,log2ratio,total : num [1:1838128] -0.057 -0.0391 -0.204 -0.7818 0.0235 ... ..$ A1955-007,log2ratio,total : num [1:1838128] 0.35 -0.241 -0.296 -0.125 -0.276 ... ..$ A1955-008,log2ratio,total : num [1:1838128] 0.60433 0.00522 0.15383 -0.23609 0.52509 ... ..$ A1955-009,log2ratio,total : num [1:1838128] -0.166 -0.247 -0.23 -0.228 -0.147 ... ..$ A1955-010,log2ratio,total : num [1:1838128] -0.0902 -0.2071 -0.109 -0.5582 0.4083 ... ..$ A1955-013,log2ratio,total : num [1:1838128] -0.2269 -0.5023 -0.1698 -0.1445 -0.0886 ... ..$ A1955-014,log2ratio,total : num [1:1838128] -0.477 -0.124 -0.131 -0.355 -0.336 ... ..$ A1955-016,log2ratio,total : num [1:1838128] -0.159 -0.193 -0.137 -0.471 -0.397 ... ..$ A1955-017,log2ratio,total : num [1:1838128] 0.3317 -0.0105 -0.0246 -0.2876 0.0301 ... ..$ A1955-018,log2ratio,total : num [1:1838128] -0.08261 -0.73078 -0.63958 -0.00545 -1.62665 ... ..$ A1955-020,log2ratio,total : num [1:1838128] -0.0506 -0.2821 -0.033 -0.3097 0.013 ... ..$ A1955-021rh,log2ratio,total : num [1:1838128] 0.0403 -0.1349 0.145 -0.5794 0.3562 ... ..$ A1955-022rh,log2ratio,total : num [1:1838128] -1.332 -0.436 -0.519 -0.621 -0.536 ... ..$ A1955-033,log2ratio,total : num [1:1838128] -0.0237 -0.2418 -0.1527 -0.5331 -0.2904 ... ..$ A1955-034,log2ratio,total : num [1:1838128] 0.504 0.155 0.109 -0.3 0.56 ... ..$ A1955-035,log2ratio,total : num [1:1838128] 1.132 0.56 0.387 -0.134 0.577 ... ..$ A1955-036,log2ratio,total : num [1:1838128] -0.697 -0.823 -0.869 -0.681 -0.872 ... ..$ A1955-038,log2ratio,total : num [1:1838128] -1.957 -0.876 -1.16 -0.35 -1.543 ... ..$ A1955-039,log2ratio,total : num [1:1838128] 0.11845 -0.04037 -0.00966 -0.52031 -0.15279 ... ..$ A1955-040,log2ratio,total : num [1:1838128] -0.383 -0.525 -0.38 -0.538 -0.594 ... ..$ A1955-041,log2ratio,total : num [1:1838128] -0.19371 -0.07626 0.00504 -0.71247 -0.80625 ... ..$ A1955-045,log2ratio,total : num [1:1838128] -0.582 -0.451 -0.603 -0.965 -0.593 ... ..$ A1955-048,log2ratio,total : num [1:1838128] 0.2329 0.1001 -0.0124 -0.22 -0.084 ... ..$ A1955-049,log2ratio,total : num [1:1838128] -0.790921 -0.000494 -0.171089 -0.448867 -0.27938 ... ..$ A1955-063,log2ratio,total : num [1:1838128] 0.00685 -0.05641 0.01217 -0.08818 -0.38536 ... ..$ A1955-066,log2ratio,total : num [1:1838128] 0.21105 -0.08305 -0.00136 -0.44698 0.26788 ... ..$ A1955-067,log2ratio,total : num [1:1838128] -1.232 -0.534 -0.794 -0.636 -0.327 ... ..$ A1955-068,log2ratio,total : num [1:1838128] 0.2177 -0.0149 -0.3721 -0.3081 -0.2028 ... ..$ A1955-070,log2ratio,total : num [1:1838128] -0.208 -0.409 -0.252 -1.754 -0.6 ... ..$ A1955-072,log2ratio,total : num [1:1838128] -0.294 -0.103 -0.208 -0.187 -0.74 ... ..$ A1955-073,log2ratio,total : num [1:1838128] -0.687 -0.329 -0.467 -0.528 -1.037 ... ..$ A1955-075,log2ratio,total : num [1:1838128] -0.296 -0.252 -0.295 -0.299 -0.267 ... ..$ A1955-076,log2ratio,total : num [1:1838128] 0.628 0.142 0.317 -0.113 0.515 ... ..$ A1955-082,log2ratio,total : num [1:1838128] -0.888 -0.65 -0.344 -0.393 -0.933 ... ..$ A1955-087,log2ratio,total : num [1:1838128] -0.833 -0.718 -0.712 -0.154 -1.153 ... ..$ A1955-088,log2ratio,total : num [1:1838128] -0.947 -0.157 -0.222 0.071 -0.219 ... ..$ A1955-090,log2ratio,total : num [1:1838128] -0.166 -0.175 -0.223 -0.494 0.32 ... ..$ A1955-091,log2ratio,total : num [1:1838128] -0.8338 -0.10223 -0.17573 -0.69368 0.00222 ... ..$ A1955-092,log2ratio,total : num [1:1838128] -0.373 -0.351 -0.344 -1.336 -0.412 ... ..$ A1955-094,log2ratio,total : num [1:1838128] -1.568 -0.8 -0.955 -0.966 -1.386 ... ..$ A1955-100rh,log2ratio,total : num [1:1838128] -0.0436 -0.0108 -0.2406 -0.0861 -0.8679 ... ..$ A1955-107,log2ratio,total : num [1:1838128] -0.468 -0.625 -0.526 -0.265 -1.518 ... ..$ A1955-113,log2ratio,total : num [1:1838128] -0.38663 -0.00468 -0.22896 -0.38714 -0.13608 ... ..$ A1955-115,log2ratio,total : num [1:1838128] 0.1611 0.0217 -0.3659 -0.471 -0.3785 ... ..$ A1955-117,log2ratio,total : num [1:1838128] -1.697 -0.258 -0.523 -0.367 -2.135 ... ..$ A1955-119,log2ratio,total : num [1:1838128] 0.2656 -0.0574 -0.1316 -0.3418 0.1352 ... ..$ A1955-122,log2ratio,total : num [1:1838128] 0.0631 0.077 0.0826 -0.1981 -0.1949 ... ..$ A1955-124,log2ratio,total : num [1:1838128] -0.185 -0.34 -0.344 0.207 -0.517 ... ..$ A1955-127,log2ratio,total : num [1:1838128] -0.792 -0.638 -0.304 -0.534 -0.562 ... ..$ A1955-128,log2ratio,total : num [1:1838128] 0.121 -0.3106 -0.0577 -0.2244 -0.3533 ... ..$ A1955-130,log2ratio,total : num [1:1838128] 0.456 0.24 -0.119 -0.182 0.549 ... ..$ A1955-132,log2ratio,total : num [1:1838128] 0.0644 0.2199 -0.1128 0.1721 -0.114 ... ..$ A1955-136,log2ratio,total : num [1:1838128] 0.383 0.116 0.185 -0.541 0.281 ... ..$ A1955-138,log2ratio,total : num [1:1838128] -0.0388 -0.3934 -0.2769 -0.0267 -0.8398 ... ..$ A1955-139,log2ratio,total : num [1:1838128] 0.108 -0.103 -0.269 -0.643 -0.109 ... ..$ A1955-145,log2ratio,total : num [1:1838128] -1.1999 0.0415 0.1443 -0.3254 -1.3377 ... ..$ A1955-147,log2ratio,total : num [1:1838128] -0.702 -0.385 -0.658 -0.668 -1.333 ... ..$ AXF_984-1266,log2ratio,total : num [1:1838128] -0.269 0.587 0.574 0.249 0.46 ... .. [list output truncated] $ Tumor_BAF :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-03,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-11,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-14,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-16,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-21,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-26,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-30,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-04,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-06,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-07,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-10,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-12,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-15,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-20,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-23,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-24,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-25,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-31,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-32,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-34,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-36,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-38,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-004,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-006rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-007,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-008,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-009,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-010,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-013,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-014,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-016,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-017,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-018,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-020,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-021rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-022rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-033,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-034,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-035,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-036,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-038,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-039,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-040,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-041,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-045,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-048,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-049,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-063,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-066,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-067,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-068,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-070,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-072,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-073,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-075,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-076,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-082,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-087,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-088,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-090,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-091,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-092,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-094,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-100rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-107,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-113,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-115,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-117,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-119,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-122,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-124,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-127,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-128,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-130,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-132,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-136,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-138,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-139,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-145,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-147,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ AXF_984-1266,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... .. [list output truncated] $ Tumor_LogR_segmented: NULL $ Tumor_BAF_segmented : NULL $ Germline_LogR : NULL $ Germline_BAF : NULL $ SNPpos :'data.frame': 1838128 obs. of 2 variables: ..$ chromosome: int [1:1838128] 1 1 1 1 1 1 1 1 1 1 ... ..$ position : int [1:1838128] 61736 61809 61824 62153 62921 62938 72705 72777 82171 82316 ... $ ch :List of 25 ..$ : int [1:146458] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:82178] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:54181] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:9192] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chr :List of 29 ..$ : int [1:75917] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:70541] 75918 75919 75920 75921 75922 75923 75924 75925 75926 75927 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:32519] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:49659] 1008415 1008416 1008417 1008418 1008419 1008420 1008421 1008422 1008423 1008424 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:21530] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:32651] 1526934 1526935 1526936 1526937 1526938 1526939 1526940 1526941 1526942 1526943 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:8944] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:248] 1877829 1877830 1877831 1877832 1877833 1877834 1877835 1877836 1877837 1877838 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chrs : int [1:25] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ gender : chr [1:228] "XX" "XX" "XX" "XX" ... $ sexchromosomes : chr [1:2] "23" "24"

str(gg) List of 2 $ germlinegenotypes: logi [1:1838128, 1:228] NA NA NA NA NA NA ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:1838128] "CN_473963" "CN_473964" "CN_473965" "CN_477984" ... .. ..$ : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ failedarrays : NULL

name: OncotestMolecularCompendium_v1.6

tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

fullName: OncotestMolecularCompendium_v1.6,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

nbrOfFiles: 228

srcFiles: A1701-01,fracB.asb A1701-02,fracB.asb A1701-03,fracB.asb A1701-05,fracB.asb A1701-09,fracB.asb A1701-11,fracB.asb A1701-14,fracB.asb A1701-16,fracB.asb A1701-17,fracB.asb A1701-18,fracB.asb A1701-19,fracB.asb A1701-21,fracB.asb A1701-22,fracB.asb A1701-26,fracB.asb A1701-27,fracB.asb A1701-30,fracB.asb A1801-01,fracB.asb A1801-02,fracB.asb A1801-04,fracB.asb A1801-05,fracB.asb A1801-06,fracB.asb A1801-07,fracB.asb A1801-09,fracB.asb A1801-10,fracB.asb A1801-12,fracB.asb A1801-15,fracB.asb A1801-17,fracB.asb A1801-18,fracB.asb A1801-19,fracB.asb A1801-20,fracB.asb A1801-22,fracB.asb A1801-23,fracB.asb A1801-24,fracB.asb A1801-25,fracB.asb A1801-27,fracB.asb A1801-31,fracB.asb A1801-32,fracB.asb A1801-34,fracB.asb A1801-36,fracB.asb A1801-38,fracB.asb A1955-004,fracB.asb A1955-006rh,fracB.asb A1955-007,fracB.asb A1955-008,fracB.asb A1955-009,fracB.asb A1955-010,fracB.asb A1955-013,fracB.asb A1955-014,fracB.asb A1955-016,fracB.asb A1955-017,fracB.asb A1955-018,fracB.asb A1955-020,fracB.asb A1955-021rh,fracB.asb A1955-022rh,fracB.asb A1955-033,fracB.asb A1955-034,fracB.asb A1955-035,fracB.asb A1955-036,fracB.asb A1955-038,fracB.asb A1955-039,fracB.asb A1955-040,fracB.asb A1955-041,fracB.asb A1955-045,fracB.asb A1955-048,fracB.asb A1955-049,fracB.asb A1955-063,fracB.asb A1955-066,fracB.asb A1955-067,fracB.asb A1955-068,fracB.asb A1955-070,fracB.asb A1955-072,fracB.asb A1955-073,fracB.asb A1955-075,fracB.asb A1955-076,fracB.asb A1955-082,fracB.asb A1955-087,fracB.asb A1955-088,fracB.asb A1955-090,fracB.asb A1955-091,fracB.asb A1955-092,fracB.asb A1955-094,fracB.asb A1955-100rh,fracB.asb A1955-107,fracB.asb A1955-113,fracB.asb A1955-115,fracB.asb A1955-117,fracB.asb A1955-119,fracB.asb A1955-122,fracB.asb A1955-124,fracB.asb A1955-127,fracB.asb A1955-128,fracB.asb A1955-130,fracB.asb A1955-132,fracB.asb A1955-136,fracB.asb A1955-138,fracB.asb A1955-139,fracB.asb A1955-145,fracB.asb A1955-147,fracB.asb AXF_984-1266,fracB.asb BXF_1258-9749,fracB.asb CEXF_633-6901,fracB.asb CNXF_498-2524,fracB.asb CXF_1034-4446,fracB.asb CXF_1086-7881,fracB.asb CXF_1096-1670,fracB.asb CXF_1103-4309,fracB.asb CXF_1297-3644,fracB.asb CXF_158-7553,fracB.asb CXF_1729-2517,fracB.asb CXF_1783-1853,fracB.asb CXF_1784-1174,fracB.asb CXF_1788-8837,fracB.asb CXF_2032-8080,fracB.asb CXF_233-2685,fracB.asb CXF_243-3450,fracB.asb CXF_260-8231,fracB.asb CXF_280-9681,fracB.asb CXF_533-7067,fracB.asb CXF_609-1110,fracB.asb CXF_676-8129,fracB.asb CXF_742-5370,fracB.asb CXF_975-3337,fracB.asb GXA_3002-5334,fracB.asb GXA_3011-8301,fracB.asb GXA_3013-1329,fracB.asb GXA_3027-4018,fracB.asb GXF_251-6477,fracB.asb GXF_281-3183,fracB.asb GXF_602-7914,fracB.asb GXF_97-9609,fracB.asb HNXF_536-3784,fracB.asb HNXF_908-7504,fracB.asb LXFA_1012-1139,fracB.asb LXFA_1041-2201,fracB.asb LXFA_1584-4190,fracB.asb LXFA_1647-3238,fracB.asb LXFA_1848-9907,fracB.asb LXFA_289-7251,fracB.asb LXFA_297-7167,fracB.asb LXFA_400-9946,fracB.asb LXFA_526-8219,fracB.asb LXFA_586-6508,fracB.asb LXFA_592-2222,fracB.asb LXFA_623-9345,fracB.asb LXFA_629-2652,fracB.asb LXFA_677-9758,fracB.asb LXFA_749-7793,fracB.asb LXFA_923-7874,fracB.asb LXFA_983-1825,fracB.asb LXFE_1022-1122,fracB.asb LXFE_1066-4986,fracB.asb LXFE_1422-8942,fracB.asb LXFE_211-5131,fracB.asb LXFE_397-1638,fracB.asb LXFE_409-8620,fracB.asb LXFE_470-6838,fracB.asb LXFE_597-4073,fracB.asb LXFE_646-7352,fracB.asb LXFE_690-2150,fracB.asb LXFE_937-5841,fracB.asb LXFL_1072-7634,fracB.asb LXFL_1121-2152,fracB.asb LXFL_1176-9949,fracB.asb LXFL_1674-2911,fracB.asb LXFL_430-2926,fracB.asb LXFL_529-6810,fracB.asb LXFL_625-2241,fracB.asb LXFS_538-3743,fracB.asb LXFS_573-1328,fracB.asb LXFS_615-5739,fracB.asb LXFS_650-9857,fracB.asb MAXF_1162-1406,fracB.asb MAXF_1322-1230,fracB.asb MAXF_1384-9459,fracB.asb MAXF_1398-4862,fracB.asb MAXF_401-9808,fracB.asb MAXF_449-8651,fracB.asb MAXF_508-1777,fracB.asb MAXF_574-4244,fracB.asb MAXF_583-3098,fracB.asb MAXF_857-3184,fracB.asb MAXF_MX1-9711,fracB.asb MEXF_1341-6216,fracB.asb MEXF_1732-7987,fracB.asb MEXF_1765-2371,fracB.asb MEXF_1792-1094,fracB.asb MEXF_1829-9933,fracB.asb MEXF_274-5165,fracB.asb MEXF_276-7909,fracB.asb MEXF_462-6609,fracB.asb MEXF_514-9135,fracB.asb MEXF_622-8283,fracB.asb MEXF_666-3786,fracB.asb MEXF_672-1172,fracB.asb MEXF_989-3233,fracB.asb OVXF_1023-5712,fracB.asb OVXF_1544-9842,fracB.asb OVXF_550-4338,fracB.asb PAXF_1657-3882,fracB.asb PAXF_1876-9329,fracB.asb PAXF_1881-8255,fracB.asb PAXF_1900-9520,fracB.asb PAXF_1965-7495,fracB.asb PAXF_1997-4821,fracB.asb PAXF_2005-5076,fracB.asb PAXF_2007-5736,fracB.asb PAXF_546-9483,fracB.asb PAXF_736-9196,fracB.asb PXF_1118-7709,fracB.asb PXF_1752-9309,fracB.asb PXF_537-1776,fracB.asb PXF_541-3557,fracB.asb PXF_698-8077,fracB.asb RXF_1003-2005,fracB.asb RXF_1183-3134,fracB.asb RXF_1220-2600,fracB.asb RXF_1393-1995,fracB.asb RXF_393-9789,fracB.asb RXF_423-8374,fracB.asb RXF_739-7683,fracB.asb SXF_117-6806,fracB.asb SXF_1186-5409,fracB.asb SXF_1301-1660,fracB.asb SXF_463-8354,fracB.asb SXF_627-8318,fracB.asb SXF_678-9969,fracB.asb TXF_593-9924,fracB.asb TXF_881-8658,fracB.asb

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names: A1701-01 A1701-02 A1701-03 A1701-05 A1701-09 A1701-11 A1701-14 A1701-16 A1701-17 A1701-18 A1701-19 A1701-21 A1701-22 A1701-26 A1701-27 A1701-30 A1801-01 A1801-02 A1801-04 A1801-05 A1801-06 A1801-07 A1801-09 A1801-10 A1801-12 A1801-15 A1801-17 A1801-18 A1801-19 A1801-20 A1801-22 A1801-23 A1801-24 A1801-25 A1801-27 A1801-31 A1801-32 A1801-34 A1801-36 A1801-38 A1955-004 A1955-006rh A1955-007 A1955-008 A1955-009 A1955-010 A1955-013 A1955-014 A1955-016 A1955-017 A1955-018 A1955-020 A1955-021rh A1955-022rh A1955-033 A1955-034 A1955-035 A1955-036 A1955-038 A1955-039 A1955-040 A1955-041 A1955-045 A1955-048 A1955-049 A1955-063 A1955-066 A1955-067 A1955-068 A1955-070 A1955-072 A1955-073 A1955-075 A1955-076 A1955-082 A1955-087 A1955-088 A1955-090 A1955-091 A1955-092 A1955-094 A1955-100rh A1955-107 A1955-113 A1955-115 A1955-117 A1955-119 A1955-122 A1955-124 A1955-127 A1955-128 A1955-130 A1955-132 A1955-136 A1955-138 A1955-139 A1955-145 A1955-147 AXF_984-1266 BXF_1258-9749 CEXF_633-6901 CNXF_498-2524 CXF_1034-4446 CXF_1086-7881 CXF_1096-1670 CXF_1103-4309 CXF_1297-3644 CXF_158-7553 CXF_1729-2517 CXF_1783-1853 CXF_1784-1174 CXF_1788-8837 CXF_2032-8080 CXF_233-2685 CXF_243-3450 CXF_260-8231 CXF_280-9681 CXF_533-7067 CXF_609-1110 CXF_676-8129 CXF_742-5370 CXF_975-3337 GXA_3002-5334 GXA_3011-8301 GXA_3013-1329 GXA_3027-4018 GXF_251-6477 GXF_281-3183 GXF_602-7914 GXF_97-9609 HNXF_536-3784 HNXF_908-7504 LXFA_1012-1139 LXFA_1041-2201 LXFA_1584-4190 LXFA_1647-3238 LXFA_1848-9907 LXFA_289-7251 LXFA_297-7167 LXFA_400-9946 LXFA_526-8219 LXFA_586-6508 LXFA_592-2222 LXFA_623-9345 LXFA_629-2652 LXFA_677-9758 LXFA_749-7793 LXFA_923-7874 LXFA_983-1825 LXFE_1022-1122 LXFE_1066-4986 LXFE_1422-8942 LXFE_211-5131 LXFE_397-1638 LXFE_409-8620 LXFE_470-6838 LXFE_597-4073 LXFE_646-7352 LXFE_690-2150 LXFE_937-5841 LXFL_1072-7634 LXFL_1121-2152 LXFL_1176-9949 LXFL_1674-2911 LXFL_430-2926 LXFL_529-6810 LXFL_625-2241 LXFS_538-3743 LXFS_573-1328 LXFS_615-5739 LXFS_650-9857 MAXF_1162-1406 MAXF_1322-1230 MAXF_1384-9459 MAXF_1398-4862 MAXF_401-9808 MAXF_449-8651 MAXF_508-1777 MAXF_574-4244 MAXF_583-3098 MAXF_857-3184 MAXF_MX1-9711 MEXF_1341-6216 MEXF_1732-7987 MEXF_1765-2371 MEXF_1792-1094 MEXF_1829-9933 MEXF_274-5165 MEXF_276-7909 MEXF_462-6609 MEXF_514-9135 MEXF_622-8283 MEXF_666-3786 MEXF_672-1172 MEXF_989-3233 OVXF_1023-5712 OVXF_1544-9842 OVXF_550-4338 PAXF_1657-3882 PAXF_1876-9329 PAXF_1881-8255 PAXF_1900-9520 PAXF_1965-7495 PAXF_1997-4821 PAXF_2005-5076 PAXF_2007-5736 PAXF_546-9483 PAXF_736-9196 PXF_1118-7709 PXF_1752-9309 PXF_537-1776 PXF_541-3557 PXF_698-8077 RXF_1003-2005 RXF_1183-3134 RXF_1220-2600 RXF_1393-1995 RXF_393-9789 RXF_423-8374 RXF_739-7683 SXF_117-6806 SXF_1186-5409 SXF_1301-1660 SXF_463-8354 SXF_627-8318 SXF_678-9969 TXF_593-9924 TXF_881-8658

tags: fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB

fullNames: A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

platform: Affymetrix

chipType: GenomeWideSNP_6,Full

nbrOfUnits: 1881415

createdOn: 2016-04-11 16:03:43 CEST

createdBy: aroma.core v3.0.0

columnTypes: character numeric numeric double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double

columnNames: unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB 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NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-789 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 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NA NA NA NA NA NA NA AFR_A02_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A04_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A06_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A08_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA N

[haasek]

Hi Thomas,

by looking at the segmentation files I can see that the row names in the logR file are wrong. For some reason, they don’t include the probe identifier anymore but are just an enumeration. Can you check at what point in the ASCAT workflow the correct probe names are lost?

Best wishes, Kerstin

On 19 Apr 2016, at 14:47, ThomasGro notifications@github.com<mailto:notifications@github.com> wrote:

Dear Kerstin, thank you for your efforts. I have attached the bzip2 compressed files. Best regards, Thomas

Von: haasek [mailto:notifications@github.com] Gesendet: Dienstag, 19. April 2016 13:47 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you tell me how the .LogR.PCFed.txt and .BAF.PCFed.txt files look like? These should be created before you run into the problematic line. I can’t think of a part in the GC correction that would cause this error. We are running it for quite some time now on multiple platforms. I hope the output of the segmentation files can give us more insight.

Best wishes, Kerstin

Kerstin Haase Postdoctoral Training Fellow The Francis Crick Institute Lincoln’s Inn Fields Laboratory 44 Lincoln’s Inn Fields London WC2A 3LY

T: +44 (0)20 7269 3087 E: Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk<http://crick.ac.uk/> W: www.crick.ac.ukhttp://www.crick.ac.uk/http://www.crick.ac.ukhttp://www.crick.ac.uk%3chttp:/www.crick.ac.uk

On 19 Apr 2016, at 08:14, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/>> wrote:

Dear Kerstin,

Thank you very much for your reply.

The actual error massage was:

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample A1701-01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

What example data would you need to reproduce the error?

I have generated the input BAF and logR files with the AROMA pipeline. I have attached the first 50 rows from those files. But I can also send you R objects from the current stage of the pipeline (before the segmentation step). See the output from the R command ‘str(ascat.bc)’ and ‘str(gg)’ also attached.

I do not belief the chromosome renaming introduced new formatting. I have done this already in the past when I run the pipeline (but without the GC correction!) with Ascat2.1 and there, no problem occurred after this step. But let me know if you want to check this. So my first thought was that the GC correction step is maybe the critical one?!

Please let me know if you need any other data.

Best regards, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Montag, 18. April 2016 17:22 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.commailto:ascat@noreply.github.commailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com<http://noreply.github.com/>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com<http://merckgroup.com/>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/http://github.com<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com>>> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

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str(ascat.bc) List of 13 $ Tumor_LogR :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,log2ratio,total : num [1:1838128] -1.064 -0.301 0.165 -0.479 -0.725 ... ..$ A1701-02,log2ratio,total : num [1:1838128] -0.58 -0.375 -0.627 0.264 -1.456 ... ..$ A1701-03,log2ratio,total : num [1:1838128] 0.5235 -0.0274 -0.0451 -0.2053 0.1705 ... ..$ A1701-05,log2ratio,total : num [1:1838128] 0.4013 0.0851 -0.0751 0.1243 -0.1684 ... ..$ A1701-09,log2ratio,total : num [1:1838128] 0.4278 -0.1472 0.099 -0.0473 0.115 ... ..$ A1701-11,log2ratio,total : num [1:1838128] -0.6213 -0.1115 -0.1067 0.0301 0.0168 ... ..$ A1701-14,log2ratio,total : num [1:1838128] -0.73718 0.16436 -0.00593 -0.18994 -0.12872 ... ..$ A1701-16,log2ratio,total : num [1:1838128] 1.216 0.531 0.587 0.446 0.887 ... ..$ A1701-17,log2ratio,total : num [1:1838128] -0.0133 0.1652 -1.3108 -0.3043 0.318 ... ..$ A1701-18,log2ratio,total : num [1:1838128] 0.862 0.494 0.438 0.494 0.356 ... ..$ A1701-19,log2ratio,total : num [1:1838128] -0.1225 -0.0208 -0.1601 -0.2568 -0.2745 ... ..$ A1701-21,log2ratio,total : num [1:1838128] 0.675 0.1214 0.0372 0.1619 0.3637 ... ..$ A1701-22,log2ratio,total : num [1:1838128] 0.45477 -0.12108 0.00612 0.21208 -0.11725 ... ..$ A1701-26,log2ratio,total : num [1:1838128] 0.53 0.173 0.177 0.139 0.353 ... ..$ A1701-27,log2ratio,total : num [1:1838128] 0.6436 0.1175 -0.1358 0.1057 -0.0642 ... ..$ A1701-30,log2ratio,total : num [1:1838128] 0.2811 -0.143 -0.2964 -0.0682 -0.4144 ... ..$ A1801-01,log2ratio,total : num [1:1838128] -0.838 -0.022 -0.164 -0.327 -0.455 ... ..$ A1801-02,log2ratio,total : num [1:1838128] -0.3592 -0.3292 -0.4102 -0.0389 -1.3263 ... ..$ A1801-04,log2ratio,total : num [1:1838128] 0.552 0.053 0.279 -0.243 0.278 ... ..$ A1801-05,log2ratio,total : num [1:1838128] -0.3404 -0.5847 -0.51 -0.0898 -0.8582 ... ..$ A1801-06,log2ratio,total : num [1:1838128] -0.0324 -0.1867 -0.2414 -0.0411 -0.2417 ... ..$ A1801-07,log2ratio,total : num [1:1838128] -1.088 -0.58 -0.807 -0.238 -1.326 ... ..$ A1801-09,log2ratio,total : num [1:1838128] -0.0377 0.3012 0.1008 -0.1002 0.3436 ... ..$ A1801-10,log2ratio,total : num [1:1838128] 0.3937 -0.1264 -0.2854 0.0529 -0.0121 ... ..$ A1801-12,log2ratio,total : num [1:1838128] 0.2033 -0.0641 0.0946 -0.3951 0.4883 ... ..$ A1801-15,log2ratio,total : num [1:1838128] 0.2587 -0.1706 -0.0245 0.0459 -0.4473 ... ..$ A1801-17,log2ratio,total : num [1:1838128] 0.168 -0.124 0.321 -0.389 0.425 ... ..$ A1801-18,log2ratio,total : num [1:1838128] 0.637 -0.067 0.168 0.378 0.569 ... ..$ A1801-19,log2ratio,total : num [1:1838128] 0.62592 0.34983 0.47753 -0.00931 0.40493 ... ..$ A1801-20,log2ratio,total : num [1:1838128] 0.0701 0.0319 0.2329 -0.0492 0.3107 ... ..$ A1801-22,log2ratio,total : num [1:1838128] -0.247 -0.44 -0.317 0.042 -0.45 ... ..$ A1801-23,log2ratio,total : num [1:1838128] 0.1952 0.0319 -0.0321 -0.3139 0.221 ... ..$ A1801-24,log2ratio,total : num [1:1838128] 0.735 0.423 0.368 0.379 0.608 ... ..$ A1801-25,log2ratio,total : num [1:1838128] -0.3614 -0.1912 -0.3167 0.0606 -1.0455 ... ..$ A1801-27,log2ratio,total : num [1:1838128] -1.349 -0.653 -1.044 -0.462 -1.377 ... ..$ A1801-31,log2ratio,total : num [1:1838128] -0.1233 -0.4566 -0.5147 0.0551 -0.6819 ... ..$ A1801-32,log2ratio,total : num [1:1838128] -0.4494 -0.161 0.0594 -0.5185 0.0791 ... ..$ A1801-34,log2ratio,total : num [1:1838128] -0.00755 -0.07866 -0.12846 -0.22865 -0.70952 ... ..$ A1801-36,log2ratio,total : num [1:1838128] -0.208 -0.136 -0.178 -0.345 -0.859 ... ..$ A1801-38,log2ratio,total : num [1:1838128] 0.2671 0.0368 -0.09 -0.1923 0.2545 ... ..$ A1955-004,log2ratio,total : num [1:1838128] 0.0519 -0.2217 -0.094 -0.4296 -0.1114 ... ..$ A1955-006rh,log2ratio,total : num [1:1838128] -0.057 -0.0391 -0.204 -0.7818 0.0235 ... ..$ A1955-007,log2ratio,total : num [1:1838128] 0.35 -0.241 -0.296 -0.125 -0.276 ... ..$ A1955-008,log2ratio,total : num [1:1838128] 0.60433 0.00522 0.15383 -0.23609 0.52509 ... ..$ A1955-009,log2ratio,total : num [1:1838128] -0.166 -0.247 -0.23 -0.228 -0.147 ... ..$ A1955-010,log2ratio,total : num [1:1838128] -0.0902 -0.2071 -0.109 -0.5582 0.4083 ... ..$ A1955-013,log2ratio,total : num [1:1838128] -0.2269 -0.5023 -0.1698 -0.1445 -0.0886 ... ..$ A1955-014,log2ratio,total : num [1:1838128] -0.477 -0.124 -0.131 -0.355 -0.336 ... ..$ A1955-016,log2ratio,total : num [1:1838128] -0.159 -0.193 -0.137 -0.471 -0.397 ... ..$ A1955-017,log2ratio,total : num [1:1838128] 0.3317 -0.0105 -0.0246 -0.2876 0.0301 ... ..$ A1955-018,log2ratio,total : num [1:1838128] -0.08261 -0.73078 -0.63958 -0.00545 -1.62665 ... ..$ A1955-020,log2ratio,total : num [1:1838128] -0.0506 -0.2821 -0.033 -0.3097 0.013 ... ..$ A1955-021rh,log2ratio,total : num [1:1838128] 0.0403 -0.1349 0.145 -0.5794 0.3562 ... ..$ A1955-022rh,log2ratio,total : num [1:1838128] -1.332 -0.436 -0.519 -0.621 -0.536 ... ..$ A1955-033,log2ratio,total : num [1:1838128] -0.0237 -0.2418 -0.1527 -0.5331 -0.2904 ... ..$ A1955-034,log2ratio,total : num [1:1838128] 0.504 0.155 0.109 -0.3 0.56 ... ..$ A1955-035,log2ratio,total : num [1:1838128] 1.132 0.56 0.387 -0.134 0.577 ... ..$ A1955-036,log2ratio,total : num [1:1838128] -0.697 -0.823 -0.869 -0.681 -0.872 ... ..$ A1955-038,log2ratio,total : num [1:1838128] -1.957 -0.876 -1.16 -0.35 -1.543 ... ..$ A1955-039,log2ratio,total : num [1:1838128] 0.11845 -0.04037 -0.00966 -0.52031 -0.15279 ... ..$ A1955-040,log2ratio,total : num [1:1838128] -0.383 -0.525 -0.38 -0.538 -0.594 ... ..$ A1955-041,log2ratio,total : num [1:1838128] -0.19371 -0.07626 0.00504 -0.71247 -0.80625 ... ..$ A1955-045,log2ratio,total : num [1:1838128] -0.582 -0.451 -0.603 -0.965 -0.593 ... ..$ A1955-048,log2ratio,total : num [1:1838128] 0.2329 0.1001 -0.0124 -0.22 -0.084 ... ..$ A1955-049,log2ratio,total : num [1:1838128] -0.790921 -0.000494 -0.171089 -0.448867 -0.27938 ... ..$ A1955-063,log2ratio,total : num [1:1838128] 0.00685 -0.05641 0.01217 -0.08818 -0.38536 ... ..$ A1955-066,log2ratio,total : num [1:1838128] 0.21105 -0.08305 -0.00136 -0.44698 0.26788 ... ..$ A1955-067,log2ratio,total : num [1:1838128] -1.232 -0.534 -0.794 -0.636 -0.327 ... ..$ A1955-068,log2ratio,total : num [1:1838128] 0.2177 -0.0149 -0.3721 -0.3081 -0.2028 ... ..$ A1955-070,log2ratio,total : num [1:1838128] -0.208 -0.409 -0.252 -1.754 -0.6 ... ..$ A1955-072,log2ratio,total : num [1:1838128] -0.294 -0.103 -0.208 -0.187 -0.74 ... ..$ A1955-073,log2ratio,total : num [1:1838128] -0.687 -0.329 -0.467 -0.528 -1.037 ... ..$ A1955-075,log2ratio,total : num [1:1838128] -0.296 -0.252 -0.295 -0.299 -0.267 ... ..$ A1955-076,log2ratio,total : num [1:1838128] 0.628 0.142 0.317 -0.113 0.515 ... ..$ A1955-082,log2ratio,total : num [1:1838128] -0.888 -0.65 -0.344 -0.393 -0.933 ... ..$ A1955-087,log2ratio,total : num [1:1838128] -0.833 -0.718 -0.712 -0.154 -1.153 ... ..$ A1955-088,log2ratio,total : num [1:1838128] -0.947 -0.157 -0.222 0.071 -0.219 ... ..$ A1955-090,log2ratio,total : num [1:1838128] -0.166 -0.175 -0.223 -0.494 0.32 ... ..$ A1955-091,log2ratio,total : num [1:1838128] -0.8338 -0.10223 -0.17573 -0.69368 0.00222 ... ..$ A1955-092,log2ratio,total : num [1:1838128] -0.373 -0.351 -0.344 -1.336 -0.412 ... ..$ A1955-094,log2ratio,total : num [1:1838128] -1.568 -0.8 -0.955 -0.966 -1.386 ... ..$ A1955-100rh,log2ratio,total : num [1:1838128] -0.0436 -0.0108 -0.2406 -0.0861 -0.8679 ... ..$ A1955-107,log2ratio,total : num [1:1838128] -0.468 -0.625 -0.526 -0.265 -1.518 ... ..$ A1955-113,log2ratio,total : num [1:1838128] -0.38663 -0.00468 -0.22896 -0.38714 -0.13608 ... ..$ A1955-115,log2ratio,total : num [1:1838128] 0.1611 0.0217 -0.3659 -0.471 -0.3785 ... ..$ A1955-117,log2ratio,total : num [1:1838128] -1.697 -0.258 -0.523 -0.367 -2.135 ... ..$ A1955-119,log2ratio,total : num [1:1838128] 0.2656 -0.0574 -0.1316 -0.3418 0.1352 ... ..$ A1955-122,log2ratio,total : num [1:1838128] 0.0631 0.077 0.0826 -0.1981 -0.1949 ... ..$ A1955-124,log2ratio,total : num [1:1838128] -0.185 -0.34 -0.344 0.207 -0.517 ... ..$ A1955-127,log2ratio,total : num [1:1838128] -0.792 -0.638 -0.304 -0.534 -0.562 ... ..$ A1955-128,log2ratio,total : num [1:1838128] 0.121 -0.3106 -0.0577 -0.2244 -0.3533 ... ..$ A1955-130,log2ratio,total : num [1:1838128] 0.456 0.24 -0.119 -0.182 0.549 ... ..$ A1955-132,log2ratio,total : num [1:1838128] 0.0644 0.2199 -0.1128 0.1721 -0.114 ... ..$ A1955-136,log2ratio,total : num [1:1838128] 0.383 0.116 0.185 -0.541 0.281 ... ..$ A1955-138,log2ratio,total : num [1:1838128] -0.0388 -0.3934 -0.2769 -0.0267 -0.8398 ... ..$ A1955-139,log2ratio,total : num [1:1838128] 0.108 -0.103 -0.269 -0.643 -0.109 ... ..$ A1955-145,log2ratio,total : num [1:1838128] -1.1999 0.0415 0.1443 -0.3254 -1.3377 ... ..$ A1955-147,log2ratio,total : num [1:1838128] -0.702 -0.385 -0.658 -0.668 -1.333 ... ..$ AXF_984-1266,log2ratio,total : num [1:1838128] -0.269 0.587 0.574 0.249 0.46 ... .. [list output truncated] $ Tumor_BAF :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-03,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-11,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-14,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-16,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-21,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-26,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-30,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-04,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-06,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-07,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-10,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-12,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-15,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-20,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-23,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-24,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-25,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-31,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-32,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-34,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-36,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-38,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-004,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-006rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-007,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-008,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-009,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-010,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-013,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-014,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-016,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-017,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-018,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-020,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-021rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-022rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-033,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-034,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-035,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-036,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-038,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-039,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-040,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-041,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-045,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-048,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-049,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-063,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-066,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-067,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-068,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-070,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-072,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-073,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-075,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-076,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-082,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-087,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-088,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-090,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-091,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-092,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-094,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-100rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-107,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-113,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-115,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-117,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-119,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-122,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-124,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-127,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-128,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-130,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-132,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-136,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-138,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-139,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-145,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-147,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ AXF_984-1266,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... .. [list output truncated] $ Tumor_LogR_segmented: NULL $ Tumor_BAF_segmented : NULL $ Germline_LogR : NULL $ Germline_BAF : NULL $ SNPpos :'data.frame': 1838128 obs. of 2 variables: ..$ chromosome: int [1:1838128] 1 1 1 1 1 1 1 1 1 1 ... ..$ position : int [1:1838128] 61736 61809 61824 62153 62921 62938 72705 72777 82171 82316 ... $ ch :List of 25 ..$ : int [1:146458] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:82178] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:54181] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:9192] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chr :List of 29 ..$ : int [1:75917] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:70541] 75918 75919 75920 75921 75922 75923 75924 75925 75926 75927 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:32519] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:49659] 1008415 1008416 1008417 1008418 1008419 1008420 1008421 1008422 1008423 1008424 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:21530] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:32651] 1526934 1526935 1526936 1526937 1526938 1526939 1526940 1526941 1526942 1526943 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:8944] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:248] 1877829 1877830 1877831 1877832 1877833 1877834 1877835 1877836 1877837 1877838 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chrs : int [1:25] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ gender : chr [1:228] "XX" "XX" "XX" "XX" ... $ sexchromosomes : chr [1:2] "23" "24"

str(gg) List of 2 $ germlinegenotypes: logi [1:1838128, 1:228] NA NA NA NA NA NA ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:1838128] "CN_473963" "CN_473964" "CN_473965" "CN_477984" ... .. ..$ : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ failedarrays : NULL

name: OncotestMolecularCompendium_v1.6

tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

fullName: OncotestMolecularCompendium_v1.6,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

nbrOfFiles: 228

srcFiles: A1701-01,fracB.asb A1701-02,fracB.asb A1701-03,fracB.asb A1701-05,fracB.asb A1701-09,fracB.asb A1701-11,fracB.asb A1701-14,fracB.asb A1701-16,fracB.asb A1701-17,fracB.asb A1701-18,fracB.asb A1701-19,fracB.asb A1701-21,fracB.asb A1701-22,fracB.asb A1701-26,fracB.asb A1701-27,fracB.asb A1701-30,fracB.asb A1801-01,fracB.asb A1801-02,fracB.asb A1801-04,fracB.asb A1801-05,fracB.asb A1801-06,fracB.asb A1801-07,fracB.asb A1801-09,fracB.asb A1801-10,fracB.asb A1801-12,fracB.asb A1801-15,fracB.asb A1801-17,fracB.asb A1801-18,fracB.asb A1801-19,fracB.asb A1801-20,fracB.asb A1801-22,fracB.asb A1801-23,fracB.asb A1801-24,fracB.asb A1801-25,fracB.asb A1801-27,fracB.asb A1801-31,fracB.asb A1801-32,fracB.asb A1801-34,fracB.asb A1801-36,fracB.asb A1801-38,fracB.asb A1955-004,fracB.asb A1955-006rh,fracB.asb A1955-007,fracB.asb A1955-008,fracB.asb A1955-009,fracB.asb A1955-010,fracB.asb A1955-013,fracB.asb A1955-014,fracB.asb A1955-016,fracB.asb A1955-017,fracB.asb A1955-018,fracB.asb A1955-020,fracB.asb A1955-021rh,fracB.asb A1955-022rh,fracB.asb A1955-033,fracB.asb A1955-034,fracB.asb A1955-035,fracB.asb A1955-036,fracB.asb A1955-038,fracB.asb A1955-039,fracB.asb A1955-040,fracB.asb A1955-041,fracB.asb A1955-045,fracB.asb A1955-048,fracB.asb A1955-049,fracB.asb A1955-063,fracB.asb A1955-066,fracB.asb A1955-067,fracB.asb A1955-068,fracB.asb A1955-070,fracB.asb A1955-072,fracB.asb A1955-073,fracB.asb A1955-075,fracB.asb A1955-076,fracB.asb A1955-082,fracB.asb A1955-087,fracB.asb A1955-088,fracB.asb A1955-090,fracB.asb A1955-091,fracB.asb A1955-092,fracB.asb A1955-094,fracB.asb A1955-100rh,fracB.asb A1955-107,fracB.asb A1955-113,fracB.asb A1955-115,fracB.asb A1955-117,fracB.asb A1955-119,fracB.asb A1955-122,fracB.asb A1955-124,fracB.asb A1955-127,fracB.asb A1955-128,fracB.asb A1955-130,fracB.asb A1955-132,fracB.asb A1955-136,fracB.asb A1955-138,fracB.asb A1955-139,fracB.asb A1955-145,fracB.asb A1955-147,fracB.asb AXF_984-1266,fracB.asb BXF_1258-9749,fracB.asb CEXF_633-6901,fracB.asb CNXF_498-2524,fracB.asb CXF_1034-4446,fracB.asb CXF_1086-7881,fracB.asb CXF_1096-1670,fracB.asb CXF_1103-4309,fracB.asb CXF_1297-3644,fracB.asb CXF_158-7553,fracB.asb CXF_1729-2517,fracB.asb CXF_1783-1853,fracB.asb CXF_1784-1174,fracB.asb CXF_1788-8837,fracB.asb CXF_2032-8080,fracB.asb CXF_233-2685,fracB.asb CXF_243-3450,fracB.asb CXF_260-8231,fracB.asb CXF_280-9681,fracB.asb CXF_533-7067,fracB.asb CXF_609-1110,fracB.asb CXF_676-8129,fracB.asb CXF_742-5370,fracB.asb CXF_975-3337,fracB.asb GXA_3002-5334,fracB.asb GXA_3011-8301,fracB.asb GXA_3013-1329,fracB.asb GXA_3027-4018,fracB.asb GXF_251-6477,fracB.asb GXF_281-3183,fracB.asb GXF_602-7914,fracB.asb GXF_97-9609,fracB.asb HNXF_536-3784,fracB.asb HNXF_908-7504,fracB.asb LXFA_1012-1139,fracB.asb LXFA_1041-2201,fracB.asb LXFA_1584-4190,fracB.asb LXFA_1647-3238,fracB.asb LXFA_1848-9907,fracB.asb LXFA_289-7251,fracB.asb LXFA_297-7167,fracB.asb LXFA_400-9946,fracB.asb LXFA_526-8219,fracB.asb LXFA_586-6508,fracB.asb LXFA_592-2222,fracB.asb LXFA_623-9345,fracB.asb LXFA_629-2652,fracB.asb LXFA_677-9758,fracB.asb LXFA_749-7793,fracB.asb LXFA_923-7874,fracB.asb LXFA_983-1825,fracB.asb LXFE_1022-1122,fracB.asb LXFE_1066-4986,fracB.asb LXFE_1422-8942,fracB.asb LXFE_211-5131,fracB.asb LXFE_397-1638,fracB.asb LXFE_409-8620,fracB.asb LXFE_470-6838,fracB.asb LXFE_597-4073,fracB.asb LXFE_646-7352,fracB.asb LXFE_690-2150,fracB.asb LXFE_937-5841,fracB.asb LXFL_1072-7634,fracB.asb LXFL_1121-2152,fracB.asb LXFL_1176-9949,fracB.asb LXFL_1674-2911,fracB.asb LXFL_430-2926,fracB.asb LXFL_529-6810,fracB.asb LXFL_625-2241,fracB.asb LXFS_538-3743,fracB.asb LXFS_573-1328,fracB.asb LXFS_615-5739,fracB.asb LXFS_650-9857,fracB.asb MAXF_1162-1406,fracB.asb MAXF_1322-1230,fracB.asb MAXF_1384-9459,fracB.asb MAXF_1398-4862,fracB.asb MAXF_401-9808,fracB.asb MAXF_449-8651,fracB.asb MAXF_508-1777,fracB.asb MAXF_574-4244,fracB.asb MAXF_583-3098,fracB.asb MAXF_857-3184,fracB.asb MAXF_MX1-9711,fracB.asb MEXF_1341-6216,fracB.asb MEXF_1732-7987,fracB.asb MEXF_1765-2371,fracB.asb MEXF_1792-1094,fracB.asb MEXF_1829-9933,fracB.asb MEXF_274-5165,fracB.asb MEXF_276-7909,fracB.asb MEXF_462-6609,fracB.asb MEXF_514-9135,fracB.asb MEXF_622-8283,fracB.asb MEXF_666-3786,fracB.asb MEXF_672-1172,fracB.asb MEXF_989-3233,fracB.asb OVXF_1023-5712,fracB.asb OVXF_1544-9842,fracB.asb OVXF_550-4338,fracB.asb PAXF_1657-3882,fracB.asb PAXF_1876-9329,fracB.asb PAXF_1881-8255,fracB.asb PAXF_1900-9520,fracB.asb PAXF_1965-7495,fracB.asb PAXF_1997-4821,fracB.asb PAXF_2005-5076,fracB.asb PAXF_2007-5736,fracB.asb PAXF_546-9483,fracB.asb PAXF_736-9196,fracB.asb PXF_1118-7709,fracB.asb PXF_1752-9309,fracB.asb PXF_537-1776,fracB.asb PXF_541-3557,fracB.asb PXF_698-8077,fracB.asb RXF_1003-2005,fracB.asb RXF_1183-3134,fracB.asb RXF_1220-2600,fracB.asb RXF_1393-1995,fracB.asb RXF_393-9789,fracB.asb RXF_423-8374,fracB.asb RXF_739-7683,fracB.asb SXF_117-6806,fracB.asb SXF_1186-5409,fracB.asb SXF_1301-1660,fracB.asb SXF_463-8354,fracB.asb SXF_627-8318,fracB.asb SXF_678-9969,fracB.asb TXF_593-9924,fracB.asb TXF_881-8658,fracB.asb

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names: A1701-01 A1701-02 A1701-03 A1701-05 A1701-09 A1701-11 A1701-14 A1701-16 A1701-17 A1701-18 A1701-19 A1701-21 A1701-22 A1701-26 A1701-27 A1701-30 A1801-01 A1801-02 A1801-04 A1801-05 A1801-06 A1801-07 A1801-09 A1801-10 A1801-12 A1801-15 A1801-17 A1801-18 A1801-19 A1801-20 A1801-22 A1801-23 A1801-24 A1801-25 A1801-27 A1801-31 A1801-32 A1801-34 A1801-36 A1801-38 A1955-004 A1955-006rh A1955-007 A1955-008 A1955-009 A1955-010 A1955-013 A1955-014 A1955-016 A1955-017 A1955-018 A1955-020 A1955-021rh A1955-022rh A1955-033 A1955-034 A1955-035 A1955-036 A1955-038 A1955-039 A1955-040 A1955-041 A1955-045 A1955-048 A1955-049 A1955-063 A1955-066 A1955-067 A1955-068 A1955-070 A1955-072 A1955-073 A1955-075 A1955-076 A1955-082 A1955-087 A1955-088 A1955-090 A1955-091 A1955-092 A1955-094 A1955-100rh A1955-107 A1955-113 A1955-115 A1955-117 A1955-119 A1955-122 A1955-124 A1955-127 A1955-128 A1955-130 A1955-132 A1955-136 A1955-138 A1955-139 A1955-145 A1955-147 AXF_984-1266 BXF_1258-9749 CEXF_633-6901 CNXF_498-2524 CXF_1034-4446 CXF_1086-7881 CXF_1096-1670 CXF_1103-4309 CXF_1297-3644 CXF_158-7553 CXF_1729-2517 CXF_1783-1853 CXF_1784-1174 CXF_1788-8837 CXF_2032-8080 CXF_233-2685 CXF_243-3450 CXF_260-8231 CXF_280-9681 CXF_533-7067 CXF_609-1110 CXF_676-8129 CXF_742-5370 CXF_975-3337 GXA_3002-5334 GXA_3011-8301 GXA_3013-1329 GXA_3027-4018 GXF_251-6477 GXF_281-3183 GXF_602-7914 GXF_97-9609 HNXF_536-3784 HNXF_908-7504 LXFA_1012-1139 LXFA_1041-2201 LXFA_1584-4190 LXFA_1647-3238 LXFA_1848-9907 LXFA_289-7251 LXFA_297-7167 LXFA_400-9946 LXFA_526-8219 LXFA_586-6508 LXFA_592-2222 LXFA_623-9345 LXFA_629-2652 LXFA_677-9758 LXFA_749-7793 LXFA_923-7874 LXFA_983-1825 LXFE_1022-1122 LXFE_1066-4986 LXFE_1422-8942 LXFE_211-5131 LXFE_397-1638 LXFE_409-8620 LXFE_470-6838 LXFE_597-4073 LXFE_646-7352 LXFE_690-2150 LXFE_937-5841 LXFL_1072-7634 LXFL_1121-2152 LXFL_1176-9949 LXFL_1674-2911 LXFL_430-2926 LXFL_529-6810 LXFL_625-2241 LXFS_538-3743 LXFS_573-1328 LXFS_615-5739 LXFS_650-9857 MAXF_1162-1406 MAXF_1322-1230 MAXF_1384-9459 MAXF_1398-4862 MAXF_401-9808 MAXF_449-8651 MAXF_508-1777 MAXF_574-4244 MAXF_583-3098 MAXF_857-3184 MAXF_MX1-9711 MEXF_1341-6216 MEXF_1732-7987 MEXF_1765-2371 MEXF_1792-1094 MEXF_1829-9933 MEXF_274-5165 MEXF_276-7909 MEXF_462-6609 MEXF_514-9135 MEXF_622-8283 MEXF_666-3786 MEXF_672-1172 MEXF_989-3233 OVXF_1023-5712 OVXF_1544-9842 OVXF_550-4338 PAXF_1657-3882 PAXF_1876-9329 PAXF_1881-8255 PAXF_1900-9520 PAXF_1965-7495 PAXF_1997-4821 PAXF_2005-5076 PAXF_2007-5736 PAXF_546-9483 PAXF_736-9196 PXF_1118-7709 PXF_1752-9309 PXF_537-1776 PXF_541-3557 PXF_698-8077 RXF_1003-2005 RXF_1183-3134 RXF_1220-2600 RXF_1393-1995 RXF_393-9789 RXF_423-8374 RXF_739-7683 SXF_117-6806 SXF_1186-5409 SXF_1301-1660 SXF_463-8354 SXF_627-8318 SXF_678-9969 TXF_593-9924 TXF_881-8658

tags: fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB

fullNames: A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

platform: Affymetrix

chipType: GenomeWideSNP_6,Full

nbrOfUnits: 1881415

createdOn: 2016-04-11 16:03:43 CEST

createdBy: aroma.core v3.0.0

columnTypes: character numeric numeric double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double

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A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB 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NA NA NA NA NA NA NA AFR_A02_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFR_A04_SB NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 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NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

[ThomasGro]

Hi Kerstin,

Hmm, I do see the correct names in my ascat.bc object:

head(rownames(ascat.bc$Tumor_LogR),5)

[1] "CN_473963" "CN_473964" "CN_473965" "CN_477984" "CN_473981" Which are used in the ascat.aspcf function as far as I can see:

put in names and write results to files

    names(logRPCFed) = rownames(ASCATobj$Tumor_LogR)

I do not know what else to check to be frank.

Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Dienstag, 19. April 2016 19:42 An: Crick-CancerGenomics/ascat ascat@noreply.github.com Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

by looking at the segmentation files I can see that the row names in the logR file are wrong. For some reason, they don’t include the probe identifier anymore but are just an enumeration. Can you check at what point in the ASCAT workflow the correct probe names are lost?

Best wishes, Kerstin

On 19 Apr 2016, at 14:47, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

Dear Kerstin, thank you for your efforts. I have attached the bzip2 compressed files. Best regards, Thomas

Von: haasek [mailto:notifications@github.com] Gesendet: Dienstag, 19. April 2016 13:47 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com<mailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you tell me how the .LogR.PCFed.txt and .BAF.PCFed.txt files look like? These should be created before you run into the problematic line. I can’t think of a part in the GC correction that would cause this error. We are running it for quite some time now on multiple platforms. I hope the output of the segmentation files can give us more insight.

Best wishes, Kerstin

Kerstin Haase Postdoctoral Training Fellow The Francis Crick Institute Lincoln’s Inn Fields Laboratory 44 Lincoln’s Inn Fields London WC2A 3LY

T: +44 (0)20 7269 3087 E: Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk<http://crick.ac.uk/<mailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3e%3cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3chttp://crick.ac.uk/>> W: www.crick.ac.ukhttp://www.crick.ac.uk/http://www.crick.ac.ukhttp://www.crick.ac.uk%3chttp:/www.crick.ac.uk<http://www.crick.ac.uk%3chttp:/www.crick.ac.uk/%3e%3chttp:/www.crick.ac.uk%3chttp:/www.crick.ac.uk%3chttp:/www.crick.ac.uk>

On 19 Apr 2016, at 08:14, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/>>> wrote:

Dear Kerstin,

Thank you very much for your reply.

The actual error massage was:

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample A1701-01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

What example data would you need to reproduce the error?

I have generated the input BAF and logR files with the AROMA pipeline. I have attached the first 50 rows from those files. But I can also send you R objects from the current stage of the pipeline (before the segmentation step). See the output from the R command ‘str(ascat.bc)’ and ‘str(gg)’ also attached.

I do not belief the chromosome renaming introduced new formatting. I have done this already in the past when I run the pipeline (but without the GC correction!) with Ascat2.1 and there, no problem occurred after this step. But let me know if you want to check this. So my first thought was that the GC correction step is maybe the critical one?!

Please let me know if you need any other data.

Best regards, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Montag, 18. April 2016 17:22 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com<mailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com>mailto:ascat@noreply.github.commailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com<http://noreply.github.com/<mailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com%3chttp://noreply.github.com/>>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com>mailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com<http://merckgroup.com/<mailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com%3chttp://merckgroup.com/>>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/>>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/http://github.commailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com<http://github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp:/github.com>>>> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

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str(ascat.bc) List of 13 $ Tumor_LogR :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,log2ratio,total : num [1:1838128] -1.064 -0.301 0.165 -0.479 -0.725 ... ..$ A1701-02,log2ratio,total : num [1:1838128] -0.58 -0.375 -0.627 0.264 -1.456 ... ..$ A1701-03,log2ratio,total : num [1:1838128] 0.5235 -0.0274 -0.0451 -0.2053 0.1705 ... ..$ A1701-05,log2ratio,total : num [1:1838128] 0.4013 0.0851 -0.0751 0.1243 -0.1684 ... ..$ A1701-09,log2ratio,total : num [1:1838128] 0.4278 -0.1472 0.099 -0.0473 0.115 ... ..$ A1701-11,log2ratio,total : num [1:1838128] -0.6213 -0.1115 -0.1067 0.0301 0.0168 ... ..$ A1701-14,log2ratio,total : num [1:1838128] -0.73718 0.16436 -0.00593 -0.18994 -0.12872 ... ..$ A1701-16,log2ratio,total : num [1:1838128] 1.216 0.531 0.587 0.446 0.887 ... ..$ A1701-17,log2ratio,total : num [1:1838128] -0.0133 0.1652 -1.3108 -0.3043 0.318 ... ..$ A1701-18,log2ratio,total : num [1:1838128] 0.862 0.494 0.438 0.494 0.356 ... ..$ A1701-19,log2ratio,total : num [1:1838128] -0.1225 -0.0208 -0.1601 -0.2568 -0.2745 ... ..$ A1701-21,log2ratio,total : num [1:1838128] 0.675 0.1214 0.0372 0.1619 0.3637 ... ..$ A1701-22,log2ratio,total : num [1:1838128] 0.45477 -0.12108 0.00612 0.21208 -0.11725 ... ..$ A1701-26,log2ratio,total : num [1:1838128] 0.53 0.173 0.177 0.139 0.353 ... ..$ A1701-27,log2ratio,total : num [1:1838128] 0.6436 0.1175 -0.1358 0.1057 -0.0642 ... ..$ A1701-30,log2ratio,total : num [1:1838128] 0.2811 -0.143 -0.2964 -0.0682 -0.4144 ... ..$ A1801-01,log2ratio,total : num [1:1838128] -0.838 -0.022 -0.164 -0.327 -0.455 ... ..$ A1801-02,log2ratio,total : num [1:1838128] -0.3592 -0.3292 -0.4102 -0.0389 -1.3263 ... ..$ A1801-04,log2ratio,total : num [1:1838128] 0.552 0.053 0.279 -0.243 0.278 ... ..$ A1801-05,log2ratio,total : num [1:1838128] -0.3404 -0.5847 -0.51 -0.0898 -0.8582 ... ..$ A1801-06,log2ratio,total : num [1:1838128] -0.0324 -0.1867 -0.2414 -0.0411 -0.2417 ... ..$ A1801-07,log2ratio,total : num [1:1838128] -1.088 -0.58 -0.807 -0.238 -1.326 ... ..$ A1801-09,log2ratio,total : num [1:1838128] -0.0377 0.3012 0.1008 -0.1002 0.3436 ... ..$ A1801-10,log2ratio,total : num [1:1838128] 0.3937 -0.1264 -0.2854 0.0529 -0.0121 ... ..$ A1801-12,log2ratio,total : num [1:1838128] 0.2033 -0.0641 0.0946 -0.3951 0.4883 ... ..$ A1801-15,log2ratio,total : num [1:1838128] 0.2587 -0.1706 -0.0245 0.0459 -0.4473 ... ..$ A1801-17,log2ratio,total : num [1:1838128] 0.168 -0.124 0.321 -0.389 0.425 ... ..$ A1801-18,log2ratio,total : num [1:1838128] 0.637 -0.067 0.168 0.378 0.569 ... ..$ A1801-19,log2ratio,total : num [1:1838128] 0.62592 0.34983 0.47753 -0.00931 0.40493 ... ..$ A1801-20,log2ratio,total : num [1:1838128] 0.0701 0.0319 0.2329 -0.0492 0.3107 ... ..$ A1801-22,log2ratio,total : num [1:1838128] -0.247 -0.44 -0.317 0.042 -0.45 ... ..$ A1801-23,log2ratio,total : num [1:1838128] 0.1952 0.0319 -0.0321 -0.3139 0.221 ... ..$ A1801-24,log2ratio,total : num [1:1838128] 0.735 0.423 0.368 0.379 0.608 ... ..$ A1801-25,log2ratio,total : num [1:1838128] -0.3614 -0.1912 -0.3167 0.0606 -1.0455 ... ..$ A1801-27,log2ratio,total : num [1:1838128] -1.349 -0.653 -1.044 -0.462 -1.377 ... ..$ A1801-31,log2ratio,total : num [1:1838128] -0.1233 -0.4566 -0.5147 0.0551 -0.6819 ... ..$ A1801-32,log2ratio,total : num [1:1838128] -0.4494 -0.161 0.0594 -0.5185 0.0791 ... ..$ A1801-34,log2ratio,total : num [1:1838128] -0.00755 -0.07866 -0.12846 -0.22865 -0.70952 ... ..$ A1801-36,log2ratio,total : num [1:1838128] -0.208 -0.136 -0.178 -0.345 -0.859 ... ..$ A1801-38,log2ratio,total : num [1:1838128] 0.2671 0.0368 -0.09 -0.1923 0.2545 ... ..$ A1955-004,log2ratio,total : num [1:1838128] 0.0519 -0.2217 -0.094 -0.4296 -0.1114 ... ..$ A1955-006rh,log2ratio,total : num [1:1838128] -0.057 -0.0391 -0.204 -0.7818 0.0235 ... ..$ A1955-007,log2ratio,total : num [1:1838128] 0.35 -0.241 -0.296 -0.125 -0.276 ... ..$ A1955-008,log2ratio,total : num [1:1838128] 0.60433 0.00522 0.15383 -0.23609 0.52509 ... ..$ A1955-009,log2ratio,total : num [1:1838128] -0.166 -0.247 -0.23 -0.228 -0.147 ... ..$ A1955-010,log2ratio,total : num [1:1838128] -0.0902 -0.2071 -0.109 -0.5582 0.4083 ... ..$ A1955-013,log2ratio,total : num [1:1838128] -0.2269 -0.5023 -0.1698 -0.1445 -0.0886 ... ..$ A1955-014,log2ratio,total : num [1:1838128] -0.477 -0.124 -0.131 -0.355 -0.336 ... ..$ A1955-016,log2ratio,total : num [1:1838128] -0.159 -0.193 -0.137 -0.471 -0.397 ... ..$ A1955-017,log2ratio,total : num [1:1838128] 0.3317 -0.0105 -0.0246 -0.2876 0.0301 ... ..$ A1955-018,log2ratio,total : num [1:1838128] -0.08261 -0.73078 -0.63958 -0.00545 -1.62665 ... ..$ A1955-020,log2ratio,total : num [1:1838128] -0.0506 -0.2821 -0.033 -0.3097 0.013 ... ..$ A1955-021rh,log2ratio,total : num [1:1838128] 0.0403 -0.1349 0.145 -0.5794 0.3562 ... ..$ A1955-022rh,log2ratio,total : num [1:1838128] -1.332 -0.436 -0.519 -0.621 -0.536 ... ..$ A1955-033,log2ratio,total : num [1:1838128] -0.0237 -0.2418 -0.1527 -0.5331 -0.2904 ... ..$ A1955-034,log2ratio,total : num [1:1838128] 0.504 0.155 0.109 -0.3 0.56 ... ..$ A1955-035,log2ratio,total : num [1:1838128] 1.132 0.56 0.387 -0.134 0.577 ... ..$ A1955-036,log2ratio,total : num [1:1838128] -0.697 -0.823 -0.869 -0.681 -0.872 ... ..$ A1955-038,log2ratio,total : num [1:1838128] -1.957 -0.876 -1.16 -0.35 -1.543 ... ..$ A1955-039,log2ratio,total : num [1:1838128] 0.11845 -0.04037 -0.00966 -0.52031 -0.15279 ... ..$ A1955-040,log2ratio,total : num [1:1838128] -0.383 -0.525 -0.38 -0.538 -0.594 ... ..$ A1955-041,log2ratio,total : num [1:1838128] -0.19371 -0.07626 0.00504 -0.71247 -0.80625 ... ..$ A1955-045,log2ratio,total : num [1:1838128] -0.582 -0.451 -0.603 -0.965 -0.593 ... ..$ A1955-048,log2ratio,total : num [1:1838128] 0.2329 0.1001 -0.0124 -0.22 -0.084 ... ..$ A1955-049,log2ratio,total : num [1:1838128] -0.790921 -0.000494 -0.171089 -0.448867 -0.27938 ... ..$ A1955-063,log2ratio,total : num [1:1838128] 0.00685 -0.05641 0.01217 -0.08818 -0.38536 ... ..$ A1955-066,log2ratio,total : num [1:1838128] 0.21105 -0.08305 -0.00136 -0.44698 0.26788 ... ..$ A1955-067,log2ratio,total : num [1:1838128] -1.232 -0.534 -0.794 -0.636 -0.327 ... ..$ A1955-068,log2ratio,total : num [1:1838128] 0.2177 -0.0149 -0.3721 -0.3081 -0.2028 ... ..$ A1955-070,log2ratio,total : num [1:1838128] -0.208 -0.409 -0.252 -1.754 -0.6 ... ..$ A1955-072,log2ratio,total : num [1:1838128] -0.294 -0.103 -0.208 -0.187 -0.74 ... ..$ A1955-073,log2ratio,total : num [1:1838128] -0.687 -0.329 -0.467 -0.528 -1.037 ... ..$ A1955-075,log2ratio,total : num [1:1838128] -0.296 -0.252 -0.295 -0.299 -0.267 ... ..$ A1955-076,log2ratio,total : num [1:1838128] 0.628 0.142 0.317 -0.113 0.515 ... ..$ A1955-082,log2ratio,total : num [1:1838128] -0.888 -0.65 -0.344 -0.393 -0.933 ... ..$ A1955-087,log2ratio,total : num [1:1838128] -0.833 -0.718 -0.712 -0.154 -1.153 ... ..$ A1955-088,log2ratio,total : num [1:1838128] -0.947 -0.157 -0.222 0.071 -0.219 ... ..$ A1955-090,log2ratio,total : num [1:1838128] -0.166 -0.175 -0.223 -0.494 0.32 ... ..$ A1955-091,log2ratio,total : num [1:1838128] -0.8338 -0.10223 -0.17573 -0.69368 0.00222 ... ..$ A1955-092,log2ratio,total : num [1:1838128] -0.373 -0.351 -0.344 -1.336 -0.412 ... ..$ A1955-094,log2ratio,total : num [1:1838128] -1.568 -0.8 -0.955 -0.966 -1.386 ... ..$ A1955-100rh,log2ratio,total : num [1:1838128] -0.0436 -0.0108 -0.2406 -0.0861 -0.8679 ... ..$ A1955-107,log2ratio,total : num [1:1838128] -0.468 -0.625 -0.526 -0.265 -1.518 ... ..$ A1955-113,log2ratio,total : num [1:1838128] -0.38663 -0.00468 -0.22896 -0.38714 -0.13608 ... ..$ A1955-115,log2ratio,total : num [1:1838128] 0.1611 0.0217 -0.3659 -0.471 -0.3785 ... ..$ A1955-117,log2ratio,total : num [1:1838128] -1.697 -0.258 -0.523 -0.367 -2.135 ... ..$ A1955-119,log2ratio,total : num [1:1838128] 0.2656 -0.0574 -0.1316 -0.3418 0.1352 ... ..$ A1955-122,log2ratio,total : num [1:1838128] 0.0631 0.077 0.0826 -0.1981 -0.1949 ... ..$ A1955-124,log2ratio,total : num [1:1838128] -0.185 -0.34 -0.344 0.207 -0.517 ... ..$ A1955-127,log2ratio,total : num [1:1838128] -0.792 -0.638 -0.304 -0.534 -0.562 ... ..$ A1955-128,log2ratio,total : num [1:1838128] 0.121 -0.3106 -0.0577 -0.2244 -0.3533 ... ..$ A1955-130,log2ratio,total : num [1:1838128] 0.456 0.24 -0.119 -0.182 0.549 ... ..$ A1955-132,log2ratio,total : num [1:1838128] 0.0644 0.2199 -0.1128 0.1721 -0.114 ... ..$ A1955-136,log2ratio,total : num [1:1838128] 0.383 0.116 0.185 -0.541 0.281 ... ..$ A1955-138,log2ratio,total : num [1:1838128] -0.0388 -0.3934 -0.2769 -0.0267 -0.8398 ... ..$ A1955-139,log2ratio,total : num [1:1838128] 0.108 -0.103 -0.269 -0.643 -0.109 ... ..$ A1955-145,log2ratio,total : num [1:1838128] -1.1999 0.0415 0.1443 -0.3254 -1.3377 ... ..$ A1955-147,log2ratio,total : num [1:1838128] -0.702 -0.385 -0.658 -0.668 -1.333 ... ..$ AXF_984-1266,log2ratio,total : num [1:1838128] -0.269 0.587 0.574 0.249 0.46 ... .. [list output truncated] $ Tumor_BAF :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-03,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-11,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-14,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-16,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-21,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-26,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-30,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-04,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-06,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-07,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-10,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-12,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-15,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-20,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-23,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-24,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-25,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-31,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-32,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-34,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-36,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-38,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-004,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-006rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-007,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-008,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-009,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-010,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-013,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-014,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-016,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-017,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-018,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-020,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-021rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-022rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-033,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-034,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-035,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-036,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-038,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-039,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-040,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-041,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-045,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-048,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-049,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-063,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-066,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-067,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-068,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-070,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-072,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-073,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-075,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-076,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-082,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-087,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-088,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-090,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-091,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-092,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-094,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-100rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-107,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-113,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-115,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-117,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-119,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-122,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-124,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-127,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-128,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-130,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-132,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-136,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-138,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-139,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-145,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-147,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ AXF_984-1266,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... .. [list output truncated] $ Tumor_LogR_segmented: NULL $ Tumor_BAF_segmented : NULL $ Germline_LogR : NULL $ Germline_BAF : NULL $ SNPpos :'data.frame': 1838128 obs. of 2 variables: ..$ chromosome: int [1:1838128] 1 1 1 1 1 1 1 1 1 1 ... ..$ position : int [1:1838128] 61736 61809 61824 62153 62921 62938 72705 72777 82171 82316 ... $ ch :List of 25 ..$ : int [1:146458] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:82178] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:54181] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:9192] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chr :List of 29 ..$ : int [1:75917] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:70541] 75918 75919 75920 75921 75922 75923 75924 75925 75926 75927 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:32519] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:49659] 1008415 1008416 1008417 1008418 1008419 1008420 1008421 1008422 1008423 1008424 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:21530] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:32651] 1526934 1526935 1526936 1526937 1526938 1526939 1526940 1526941 1526942 1526943 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:8944] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:248] 1877829 1877830 1877831 1877832 1877833 1877834 1877835 1877836 1877837 1877838 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chrs : int [1:25] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ gender : chr [1:228] "XX" "XX" "XX" "XX" ... $ sexchromosomes : chr [1:2] "23" "24"

str(gg) List of 2 $ germlinegenotypes: logi [1:1838128, 1:228] NA NA NA NA NA NA ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:1838128] "CN_473963" "CN_473964" "CN_473965" "CN_477984" ... .. ..$ : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ failedarrays : NULL

name: OncotestMolecularCompendium_v1.6

tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

fullName: OncotestMolecularCompendium_v1.6,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

nbrOfFiles: 228

srcFiles: A1701-01,fracB.asb A1701-02,fracB.asb A1701-03,fracB.asb A1701-05,fracB.asb A1701-09,fracB.asb A1701-11,fracB.asb A1701-14,fracB.asb A1701-16,fracB.asb A1701-17,fracB.asb A1701-18,fracB.asb A1701-19,fracB.asb A1701-21,fracB.asb A1701-22,fracB.asb A1701-26,fracB.asb A1701-27,fracB.asb A1701-30,fracB.asb A1801-01,fracB.asb A1801-02,fracB.asb A1801-04,fracB.asb A1801-05,fracB.asb A1801-06,fracB.asb A1801-07,fracB.asb A1801-09,fracB.asb A1801-10,fracB.asb A1801-12,fracB.asb A1801-15,fracB.asb A1801-17,fracB.asb A1801-18,fracB.asb A1801-19,fracB.asb A1801-20,fracB.asb A1801-22,fracB.asb A1801-23,fracB.asb A1801-24,fracB.asb A1801-25,fracB.asb A1801-27,fracB.asb A1801-31,fracB.asb A1801-32,fracB.asb A1801-34,fracB.asb A1801-36,fracB.asb A1801-38,fracB.asb A1955-004,fracB.asb A1955-006rh,fracB.asb A1955-007,fracB.asb A1955-008,fracB.asb A1955-009,fracB.asb A1955-010,fracB.asb A1955-013,fracB.asb A1955-014,fracB.asb A1955-016,fracB.asb A1955-017,fracB.asb A1955-018,fracB.asb 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SXF_627-8318,fracB.asb SXF_678-9969,fracB.asb TXF_593-9924,fracB.asb TXF_881-8658,fracB.asb

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names: A1701-01 A1701-02 A1701-03 A1701-05 A1701-09 A1701-11 A1701-14 A1701-16 A1701-17 A1701-18 A1701-19 A1701-21 A1701-22 A1701-26 A1701-27 A1701-30 A1801-01 A1801-02 A1801-04 A1801-05 A1801-06 A1801-07 A1801-09 A1801-10 A1801-12 A1801-15 A1801-17 A1801-18 A1801-19 A1801-20 A1801-22 A1801-23 A1801-24 A1801-25 A1801-27 A1801-31 A1801-32 A1801-34 A1801-36 A1801-38 A1955-004 A1955-006rh A1955-007 A1955-008 A1955-009 A1955-010 A1955-013 A1955-014 A1955-016 A1955-017 A1955-018 A1955-020 A1955-021rh A1955-022rh A1955-033 A1955-034 A1955-035 A1955-036 A1955-038 A1955-039 A1955-040 A1955-041 A1955-045 A1955-048 A1955-049 A1955-063 A1955-066 A1955-067 A1955-068 A1955-070 A1955-072 A1955-073 A1955-075 A1955-076 A1955-082 A1955-087 A1955-088 A1955-090 A1955-091 A1955-092 A1955-094 A1955-100rh A1955-107 A1955-113 A1955-115 A1955-117 A1955-119 A1955-122 A1955-124 A1955-127 A1955-128 A1955-130 A1955-132 A1955-136 A1955-138 A1955-139 A1955-145 A1955-147 AXF_984-1266 BXF_1258-9749 CEXF_633-6901 CNXF_498-2524 CXF_1034-4446 CXF_1086-7881 CXF_1096-1670 CXF_1103-4309 CXF_1297-3644 CXF_158-7553 CXF_1729-2517 CXF_1783-1853 CXF_1784-1174 CXF_1788-8837 CXF_2032-8080 CXF_233-2685 CXF_243-3450 CXF_260-8231 CXF_280-9681 CXF_533-7067 CXF_609-1110 CXF_676-8129 CXF_742-5370 CXF_975-3337 GXA_3002-5334 GXA_3011-8301 GXA_3013-1329 GXA_3027-4018 GXF_251-6477 GXF_281-3183 GXF_602-7914 GXF_97-9609 HNXF_536-3784 HNXF_908-7504 LXFA_1012-1139 LXFA_1041-2201 LXFA_1584-4190 LXFA_1647-3238 LXFA_1848-9907 LXFA_289-7251 LXFA_297-7167 LXFA_400-9946 LXFA_526-8219 LXFA_586-6508 LXFA_592-2222 LXFA_623-9345 LXFA_629-2652 LXFA_677-9758 LXFA_749-7793 LXFA_923-7874 LXFA_983-1825 LXFE_1022-1122 LXFE_1066-4986 LXFE_1422-8942 LXFE_211-5131 LXFE_397-1638 LXFE_409-8620 LXFE_470-6838 LXFE_597-4073 LXFE_646-7352 LXFE_690-2150 LXFE_937-5841 LXFL_1072-7634 LXFL_1121-2152 LXFL_1176-9949 LXFL_1674-2911 LXFL_430-2926 LXFL_529-6810 LXFL_625-2241 LXFS_538-3743 LXFS_573-1328 LXFS_615-5739 LXFS_650-9857 MAXF_1162-1406 MAXF_1322-1230 MAXF_1384-9459 MAXF_1398-4862 MAXF_401-9808 MAXF_449-8651 MAXF_508-1777 MAXF_574-4244 MAXF_583-3098 MAXF_857-3184 MAXF_MX1-9711 MEXF_1341-6216 MEXF_1732-7987 MEXF_1765-2371 MEXF_1792-1094 MEXF_1829-9933 MEXF_274-5165 MEXF_276-7909 MEXF_462-6609 MEXF_514-9135 MEXF_622-8283 MEXF_666-3786 MEXF_672-1172 MEXF_989-3233 OVXF_1023-5712 OVXF_1544-9842 OVXF_550-4338 PAXF_1657-3882 PAXF_1876-9329 PAXF_1881-8255 PAXF_1900-9520 PAXF_1965-7495 PAXF_1997-4821 PAXF_2005-5076 PAXF_2007-5736 PAXF_546-9483 PAXF_736-9196 PXF_1118-7709 PXF_1752-9309 PXF_537-1776 PXF_541-3557 PXF_698-8077 RXF_1003-2005 RXF_1183-3134 RXF_1220-2600 RXF_1393-1995 RXF_393-9789 RXF_423-8374 RXF_739-7683 SXF_117-6806 SXF_1186-5409 SXF_1301-1660 SXF_463-8354 SXF_627-8318 SXF_678-9969 TXF_593-9924 TXF_881-8658

tags: fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB

fullNames: A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

platform: Affymetrix

chipType: GenomeWideSNP_6,Full

nbrOfUnits: 1881415

createdOn: 2016-04-11 16:03:43 CEST

createdBy: aroma.core v3.0.0

columnTypes: character numeric numeric double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double

columnNames: unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB AFFX-5Q-123 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-456 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFFX-5Q-789 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

[haasek]

Hi Thomas,

that is strange indeed. Is it possible that you provide me with the logR and BAF input for one sample, so I can pay around with it? Your only change to the GC correction is the change of “X” to “23” in the provided file, correct? Then I could check if I can replicate the problem here.

Best wishes, Kerstin

On 20 Apr 2016, at 08:53, ThomasGro notifications@github.com<mailto:notifications@github.com> wrote:

Hi Kerstin,

Hmm, I do see the correct names in my ascat.bc object:

head(rownames(ascat.bc$Tumor_LogR),5)

[1] "CN_473963" "CN_473964" "CN_473965" "CN_477984" "CN_473981" Which are used in the ascat.aspcf function as far as I can see:

put in names and write results to files

names(logRPCFed) = rownames(ASCATobj$Tumor_LogR)

I do not know what else to check to be frank.

Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Dienstag, 19. April 2016 19:42 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

by looking at the segmentation files I can see that the row names in the logR file are wrong. For some reason, they don’t include the probe identifier anymore but are just an enumeration. Can you check at what point in the ASCAT workflow the correct probe names are lost?

Best wishes, Kerstin

On 19 Apr 2016, at 14:47, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/>> wrote:

Dear Kerstin, thank you for your efforts. I have attached the bzip2 compressed files. Best regards, Thomas

Von: haasek [mailto:notifications@github.com] Gesendet: Dienstag, 19. April 2016 13:47 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.commailto:ascat@noreply.github.commailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com<http://noreply.github.com/>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com<http://merckgroup.com/>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you tell me how the .LogR.PCFed.txt and .BAF.PCFed.txt files look like? These should be created before you run into the problematic line. I can’t think of a part in the GC correction that would cause this error. We are running it for quite some time now on multiple platforms. I hope the output of the segmentation files can give us more insight.

Best wishes, Kerstin

Kerstin Haase Postdoctoral Training Fellow The Francis Crick Institute Lincoln’s Inn Fields Laboratory 44 Lincoln’s Inn Fields London WC2A 3LY

T: +44 (0)20 7269 3087 E: Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.ukmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk<http://crick.ac.uk/http://crick.ac.uk/<mailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3e%3cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3chttp://crick.ac.uk/>>http://crick.ac.uk/%3Cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3e%3cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3cmailto:Kerstin.Haase@crick.ac.uk%3chttp://crick.ac.uk/%3E%3E%3E%3E W: www.crick.ac.ukhttp://www.crick.ac.uk/http://www.crick.ac.uk/http://www.crick.ac.ukhttp://www.crick.ac.uk%3chttp:/www.crick.ac.uk<http://www.crick.ac.uk%3chttp:/www.crick.ac.uk/%3e%3chttp:/www.crick.ac.uk%3chttp:/www.crick.ac.uk%3chttp:/www.crick.ac.uk>

On 19 Apr 2016, at 08:14, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/http://github.com/<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/>>http://github.com/%3Cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/%3E%3E%3E%3E> wrote:

Dear Kerstin,

Thank you very much for your reply.

The actual error massage was:

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample A1701-01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

What example data would you need to reproduce the error?

I have generated the input BAF and logR files with the AROMA pipeline. I have attached the first 50 rows from those files. But I can also send you R objects from the current stage of the pipeline (before the segmentation step). See the output from the R command ‘str(ascat.bc)’ and ‘str(gg)’ also attached.

I do not belief the chromosome renaming introduced new formatting. I have done this already in the past when I run the pipeline (but without the GC correction!) with Ascat2.1 and there, no problem occurred after this step. But let me know if you want to check this. So my first thought was that the GC correction step is maybe the critical one?!

Please let me know if you need any other data.

Best regards, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Montag, 18. April 2016 17:22 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.commailto:ascat@noreply.github.commailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com<http://noreply.github.com/>mailto:ascat@noreply.github.commailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com<http://noreply.github.com/http://noreply.github.com/<mailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com%3chttp://noreply.github.com/>>http://noreply.github.com/%3Cmailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com%3chttp://noreply.github.com/%3E%3E%3E%3E> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com<http://merckgroup.com/>mailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com<http://merckgroup.com/http://merckgroup.com/<mailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com%3chttp://merckgroup.com/>>http://merckgroup.com/%3Cmailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com%3chttp://merckgroup.com/%3E%3E%3E%3E> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Dear Thomas,

could you maybe provide a minimal example that triggers your problem? I don’t think it is the renaming of the sex chromosome, as I just tried that and I couldn’t reproduce your error. Is there maybe some different formatting introduced during your renaming step? Something else that caught my eye is your sample name “Sample 01,log2ratio,total”. Is that really the correct header in your file, or is it not splitting up the different columns correctly?

Best wishes, Kerstin

On 18 Apr 2016, at 14:27, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/http://github.com/<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/>>mailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com/<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/http://github.com/%3Cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/%3E%3E%3E%3E%3Cmailto:notifications@github.com%3Cmailto:notifications@github.com%3cmailto:notifications@github.com%3Chttp://github.com/%3Cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com/%3Ehttp://github.commailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp://github.com<http://github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3chttp:/github.com>>>> wrote:

##################################################

use ASCAT 2.4 without matched normal data

##################################################

run ASCAT without matched normals (assuming AffySNP6 data, for other platforms please check our website)

TG 2016-04-12 GC correction added to pipeline

TG 2016-04-12 GC correction file for AffySNP6 has to changed for chrX naming to 23 for use with AROMA output

ascat.bc = ascat.loadData("Tumor_logR.txt","Tumor_BAF.txt") ascat.bc <- ascat.GCcorrect(ascat.bc, "GC_AffySNP6_102015_Xto23.txt") ascat.plotRawData(ascat.bc) gg<-ascat.predictGermlineGenotypes(ascat.bc, platform = "AffySNP6") ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg)

failed with

ascat.bc = ascat.aspcf(ascat.bc, ascat.gg=gg) [1] Sample 01,log2ratio,total (1/228) Error in Tumor_LogR_segmented[, sample] = logRPCFed : number of items to replace is not a multiple of replacement length

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str(ascat.bc) List of 13 $ Tumor_LogR :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,log2ratio,total : num [1:1838128] -1.064 -0.301 0.165 -0.479 -0.725 ... ..$ A1701-02,log2ratio,total : num [1:1838128] -0.58 -0.375 -0.627 0.264 -1.456 ... ..$ A1701-03,log2ratio,total : num [1:1838128] 0.5235 -0.0274 -0.0451 -0.2053 0.1705 ... ..$ A1701-05,log2ratio,total : num [1:1838128] 0.4013 0.0851 -0.0751 0.1243 -0.1684 ... ..$ A1701-09,log2ratio,total : num [1:1838128] 0.4278 -0.1472 0.099 -0.0473 0.115 ... ..$ A1701-11,log2ratio,total : num [1:1838128] -0.6213 -0.1115 -0.1067 0.0301 0.0168 ... ..$ A1701-14,log2ratio,total : num [1:1838128] -0.73718 0.16436 -0.00593 -0.18994 -0.12872 ... ..$ A1701-16,log2ratio,total : num [1:1838128] 1.216 0.531 0.587 0.446 0.887 ... ..$ A1701-17,log2ratio,total : num [1:1838128] -0.0133 0.1652 -1.3108 -0.3043 0.318 ... ..$ A1701-18,log2ratio,total : num [1:1838128] 0.862 0.494 0.438 0.494 0.356 ... ..$ A1701-19,log2ratio,total : num [1:1838128] -0.1225 -0.0208 -0.1601 -0.2568 -0.2745 ... ..$ A1701-21,log2ratio,total : num [1:1838128] 0.675 0.1214 0.0372 0.1619 0.3637 ... ..$ A1701-22,log2ratio,total : num [1:1838128] 0.45477 -0.12108 0.00612 0.21208 -0.11725 ... ..$ A1701-26,log2ratio,total : num [1:1838128] 0.53 0.173 0.177 0.139 0.353 ... ..$ A1701-27,log2ratio,total : num [1:1838128] 0.6436 0.1175 -0.1358 0.1057 -0.0642 ... ..$ A1701-30,log2ratio,total : num [1:1838128] 0.2811 -0.143 -0.2964 -0.0682 -0.4144 ... ..$ A1801-01,log2ratio,total : num [1:1838128] -0.838 -0.022 -0.164 -0.327 -0.455 ... ..$ A1801-02,log2ratio,total : num [1:1838128] -0.3592 -0.3292 -0.4102 -0.0389 -1.3263 ... ..$ A1801-04,log2ratio,total : num [1:1838128] 0.552 0.053 0.279 -0.243 0.278 ... ..$ A1801-05,log2ratio,total : num [1:1838128] -0.3404 -0.5847 -0.51 -0.0898 -0.8582 ... ..$ A1801-06,log2ratio,total : num [1:1838128] -0.0324 -0.1867 -0.2414 -0.0411 -0.2417 ... ..$ A1801-07,log2ratio,total : num [1:1838128] -1.088 -0.58 -0.807 -0.238 -1.326 ... ..$ A1801-09,log2ratio,total : num [1:1838128] -0.0377 0.3012 0.1008 -0.1002 0.3436 ... ..$ A1801-10,log2ratio,total : num [1:1838128] 0.3937 -0.1264 -0.2854 0.0529 -0.0121 ... ..$ A1801-12,log2ratio,total : num [1:1838128] 0.2033 -0.0641 0.0946 -0.3951 0.4883 ... ..$ A1801-15,log2ratio,total : num [1:1838128] 0.2587 -0.1706 -0.0245 0.0459 -0.4473 ... ..$ A1801-17,log2ratio,total : num [1:1838128] 0.168 -0.124 0.321 -0.389 0.425 ... ..$ A1801-18,log2ratio,total : num [1:1838128] 0.637 -0.067 0.168 0.378 0.569 ... ..$ A1801-19,log2ratio,total : num [1:1838128] 0.62592 0.34983 0.47753 -0.00931 0.40493 ... ..$ A1801-20,log2ratio,total : num [1:1838128] 0.0701 0.0319 0.2329 -0.0492 0.3107 ... ..$ A1801-22,log2ratio,total : num [1:1838128] -0.247 -0.44 -0.317 0.042 -0.45 ... ..$ A1801-23,log2ratio,total : num [1:1838128] 0.1952 0.0319 -0.0321 -0.3139 0.221 ... ..$ A1801-24,log2ratio,total : num [1:1838128] 0.735 0.423 0.368 0.379 0.608 ... ..$ A1801-25,log2ratio,total : num [1:1838128] -0.3614 -0.1912 -0.3167 0.0606 -1.0455 ... ..$ A1801-27,log2ratio,total : num [1:1838128] -1.349 -0.653 -1.044 -0.462 -1.377 ... ..$ A1801-31,log2ratio,total : num [1:1838128] -0.1233 -0.4566 -0.5147 0.0551 -0.6819 ... ..$ A1801-32,log2ratio,total : num [1:1838128] -0.4494 -0.161 0.0594 -0.5185 0.0791 ... ..$ A1801-34,log2ratio,total : num [1:1838128] -0.00755 -0.07866 -0.12846 -0.22865 -0.70952 ... ..$ A1801-36,log2ratio,total : num [1:1838128] -0.208 -0.136 -0.178 -0.345 -0.859 ... ..$ A1801-38,log2ratio,total : num [1:1838128] 0.2671 0.0368 -0.09 -0.1923 0.2545 ... ..$ A1955-004,log2ratio,total : num [1:1838128] 0.0519 -0.2217 -0.094 -0.4296 -0.1114 ... ..$ A1955-006rh,log2ratio,total : num [1:1838128] -0.057 -0.0391 -0.204 -0.7818 0.0235 ... ..$ A1955-007,log2ratio,total : num [1:1838128] 0.35 -0.241 -0.296 -0.125 -0.276 ... ..$ A1955-008,log2ratio,total : num [1:1838128] 0.60433 0.00522 0.15383 -0.23609 0.52509 ... ..$ A1955-009,log2ratio,total : num [1:1838128] -0.166 -0.247 -0.23 -0.228 -0.147 ... ..$ A1955-010,log2ratio,total : num [1:1838128] -0.0902 -0.2071 -0.109 -0.5582 0.4083 ... ..$ A1955-013,log2ratio,total : num [1:1838128] -0.2269 -0.5023 -0.1698 -0.1445 -0.0886 ... ..$ A1955-014,log2ratio,total : num [1:1838128] -0.477 -0.124 -0.131 -0.355 -0.336 ... ..$ A1955-016,log2ratio,total : num [1:1838128] -0.159 -0.193 -0.137 -0.471 -0.397 ... ..$ A1955-017,log2ratio,total : num [1:1838128] 0.3317 -0.0105 -0.0246 -0.2876 0.0301 ... ..$ A1955-018,log2ratio,total : num [1:1838128] -0.08261 -0.73078 -0.63958 -0.00545 -1.62665 ... ..$ A1955-020,log2ratio,total : num [1:1838128] -0.0506 -0.2821 -0.033 -0.3097 0.013 ... ..$ A1955-021rh,log2ratio,total : num [1:1838128] 0.0403 -0.1349 0.145 -0.5794 0.3562 ... ..$ A1955-022rh,log2ratio,total : num [1:1838128] -1.332 -0.436 -0.519 -0.621 -0.536 ... ..$ A1955-033,log2ratio,total : num [1:1838128] -0.0237 -0.2418 -0.1527 -0.5331 -0.2904 ... ..$ A1955-034,log2ratio,total : num [1:1838128] 0.504 0.155 0.109 -0.3 0.56 ... ..$ A1955-035,log2ratio,total : num [1:1838128] 1.132 0.56 0.387 -0.134 0.577 ... ..$ A1955-036,log2ratio,total : num [1:1838128] -0.697 -0.823 -0.869 -0.681 -0.872 ... ..$ A1955-038,log2ratio,total : num [1:1838128] -1.957 -0.876 -1.16 -0.35 -1.543 ... ..$ A1955-039,log2ratio,total : num [1:1838128] 0.11845 -0.04037 -0.00966 -0.52031 -0.15279 ... ..$ A1955-040,log2ratio,total : num [1:1838128] -0.383 -0.525 -0.38 -0.538 -0.594 ... ..$ A1955-041,log2ratio,total : num [1:1838128] -0.19371 -0.07626 0.00504 -0.71247 -0.80625 ... ..$ A1955-045,log2ratio,total : num [1:1838128] -0.582 -0.451 -0.603 -0.965 -0.593 ... ..$ A1955-048,log2ratio,total : num [1:1838128] 0.2329 0.1001 -0.0124 -0.22 -0.084 ... ..$ A1955-049,log2ratio,total : num [1:1838128] -0.790921 -0.000494 -0.171089 -0.448867 -0.27938 ... ..$ A1955-063,log2ratio,total : num [1:1838128] 0.00685 -0.05641 0.01217 -0.08818 -0.38536 ... ..$ A1955-066,log2ratio,total : num [1:1838128] 0.21105 -0.08305 -0.00136 -0.44698 0.26788 ... ..$ A1955-067,log2ratio,total : num [1:1838128] -1.232 -0.534 -0.794 -0.636 -0.327 ... ..$ A1955-068,log2ratio,total : num [1:1838128] 0.2177 -0.0149 -0.3721 -0.3081 -0.2028 ... ..$ A1955-070,log2ratio,total : num [1:1838128] -0.208 -0.409 -0.252 -1.754 -0.6 ... ..$ A1955-072,log2ratio,total : num [1:1838128] -0.294 -0.103 -0.208 -0.187 -0.74 ... ..$ A1955-073,log2ratio,total : num [1:1838128] -0.687 -0.329 -0.467 -0.528 -1.037 ... ..$ A1955-075,log2ratio,total : num [1:1838128] -0.296 -0.252 -0.295 -0.299 -0.267 ... ..$ A1955-076,log2ratio,total : num [1:1838128] 0.628 0.142 0.317 -0.113 0.515 ... ..$ A1955-082,log2ratio,total : num [1:1838128] -0.888 -0.65 -0.344 -0.393 -0.933 ... ..$ A1955-087,log2ratio,total : num [1:1838128] -0.833 -0.718 -0.712 -0.154 -1.153 ... ..$ A1955-088,log2ratio,total : num [1:1838128] -0.947 -0.157 -0.222 0.071 -0.219 ... ..$ A1955-090,log2ratio,total : num [1:1838128] -0.166 -0.175 -0.223 -0.494 0.32 ... ..$ A1955-091,log2ratio,total : num [1:1838128] -0.8338 -0.10223 -0.17573 -0.69368 0.00222 ... ..$ A1955-092,log2ratio,total : num [1:1838128] -0.373 -0.351 -0.344 -1.336 -0.412 ... ..$ A1955-094,log2ratio,total : num [1:1838128] -1.568 -0.8 -0.955 -0.966 -1.386 ... ..$ A1955-100rh,log2ratio,total : num [1:1838128] -0.0436 -0.0108 -0.2406 -0.0861 -0.8679 ... ..$ A1955-107,log2ratio,total : num [1:1838128] -0.468 -0.625 -0.526 -0.265 -1.518 ... ..$ A1955-113,log2ratio,total : num [1:1838128] -0.38663 -0.00468 -0.22896 -0.38714 -0.13608 ... ..$ A1955-115,log2ratio,total : num [1:1838128] 0.1611 0.0217 -0.3659 -0.471 -0.3785 ... ..$ A1955-117,log2ratio,total : num [1:1838128] -1.697 -0.258 -0.523 -0.367 -2.135 ... ..$ A1955-119,log2ratio,total : num [1:1838128] 0.2656 -0.0574 -0.1316 -0.3418 0.1352 ... ..$ A1955-122,log2ratio,total : num [1:1838128] 0.0631 0.077 0.0826 -0.1981 -0.1949 ... ..$ A1955-124,log2ratio,total : num [1:1838128] -0.185 -0.34 -0.344 0.207 -0.517 ... ..$ A1955-127,log2ratio,total : num [1:1838128] -0.792 -0.638 -0.304 -0.534 -0.562 ... ..$ A1955-128,log2ratio,total : num [1:1838128] 0.121 -0.3106 -0.0577 -0.2244 -0.3533 ... ..$ A1955-130,log2ratio,total : num [1:1838128] 0.456 0.24 -0.119 -0.182 0.549 ... ..$ A1955-132,log2ratio,total : num [1:1838128] 0.0644 0.2199 -0.1128 0.1721 -0.114 ... ..$ A1955-136,log2ratio,total : num [1:1838128] 0.383 0.116 0.185 -0.541 0.281 ... ..$ A1955-138,log2ratio,total : num [1:1838128] -0.0388 -0.3934 -0.2769 -0.0267 -0.8398 ... ..$ A1955-139,log2ratio,total : num [1:1838128] 0.108 -0.103 -0.269 -0.643 -0.109 ... ..$ A1955-145,log2ratio,total : num [1:1838128] -1.1999 0.0415 0.1443 -0.3254 -1.3377 ... ..$ A1955-147,log2ratio,total : num [1:1838128] -0.702 -0.385 -0.658 -0.668 -1.333 ... ..$ AXF_984-1266,log2ratio,total : num [1:1838128] -0.269 0.587 0.574 0.249 0.46 ... .. [list output truncated] $ Tumor_BAF :'data.frame': 1838128 obs. of 228 variables: ..$ A1701-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-03,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-11,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-14,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-16,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-21,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-26,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1701-30,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-01,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-02,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-04,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-05,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-06,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-07,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-09,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-10,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-12,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-15,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-17,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-18,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-19,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-20,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-22,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-23,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-24,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-25,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-27,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-31,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-32,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-34,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-36,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1801-38,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-004,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-006rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-007,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-008,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-009,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-010,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-013,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-014,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-016,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-017,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-018,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-020,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-021rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-022rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-033,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-034,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-035,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-036,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-038,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-039,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-040,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-041,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-045,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-048,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-049,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-063,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-066,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-067,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-068,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-070,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-072,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-073,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-075,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-076,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-082,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-087,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-088,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-090,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-091,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-092,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-094,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-100rh,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-107,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-113,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-115,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-117,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-119,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-122,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-124,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-127,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-128,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-130,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-132,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-136,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-138,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-139,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-145,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ A1955-147,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... ..$ AXF_984-1266,fracB : num [1:1838128] NA NA NA NA NA NA NA NA NA NA ... .. [list output truncated] $ Tumor_LogR_segmented: NULL $ Tumor_BAF_segmented : NULL $ Germline_LogR : NULL $ Germline_BAF : NULL $ SNPpos :'data.frame': 1838128 obs. of 2 variables: ..$ chromosome: int [1:1838128] 1 1 1 1 1 1 1 1 1 1 ... ..$ position : int [1:1838128] 61736 61809 61824 62153 62921 62938 72705 72777 82171 82316 ... $ ch :List of 25 ..$ : int [1:146458] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:82178] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:54181] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:9192] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chr :List of 29 ..$ : int [1:75917] 1 2 3 4 5 6 7 8 9 10 ... ..$ : int [1:70541] 75918 75919 75920 75921 75922 75923 75924 75925 75926 75927 ... ..$ : int [1:153641] 146459 146460 146461 146462 146463 146464 146465 146466 146467 146468 ... ..$ : int [1:127776] 300100 300101 300102 300103 300104 300105 300106 300107 300108 300109 ... ..$ : int [1:120351] 427876 427877 427878 427879 427880 427881 427882 427883 427884 427885 ... ..$ : int [1:115709] 548227 548228 548229 548230 548231 548232 548233 548234 548235 548236 ... ..$ : int [1:112858] 663936 663937 663938 663939 663940 663941 663942 663943 663944 663945 ... ..$ : int [1:100828] 776794 776795 776796 776797 776798 776799 776800 776801 776802 776803 ... ..$ : int [1:98274] 877622 877623 877624 877625 877626 877627 877628 877629 877630 877631 ... ..$ : int [1:32519] 975896 975897 975898 975899 975900 975901 975902 975903 975904 975905 ... ..$ : int [1:49659] 1008415 1008416 1008417 1008418 1008419 1008420 1008421 1008422 1008423 1008424 ... ..$ : int [1:93627] 1058074 1058075 1058076 1058077 1058078 1058079 1058080 1058081 1058082 1058083 ... ..$ : int [1:89604] 1151701 1151702 1151703 1151704 1151705 1151706 1151707 1151708 1151709 1151710 ... ..$ : int [1:87336] 1241305 1241306 1241307 1241308 1241309 1241310 1241311 1241312 1241313 1241314 ... ..$ : int [1:66091] 1328641 1328642 1328643 1328644 1328645 1328646 1328647 1328648 1328649 1328650 ... ..$ : int [1:57118] 1394732 1394733 1394734 1394735 1394736 1394737 1394738 1394739 1394740 1394741 ... ..$ : int [1:53554] 1451850 1451851 1451852 1451853 1451854 1451855 1451856 1451857 1451858 1451859 ... ..$ : int [1:21530] 1505404 1505405 1505406 1505407 1505408 1505409 1505410 1505411 1505412 1505413 ... ..$ : int [1:32651] 1526934 1526935 1526936 1526937 1526938 1526939 1526940 1526941 1526942 1526943 ... ..$ : int [1:46590] 1559585 1559586 1559587 1559588 1559589 1559590 1559591 1559592 1559593 1559594 ... ..$ : int [1:52103] 1606175 1606176 1606177 1606178 1606179 1606180 1606181 1606182 1606183 1606184 ... ..$ : int [1:30362] 1658278 1658279 1658280 1658281 1658282 1658283 1658284 1658285 1658286 1658287 ... ..$ : int [1:43647] 1688640 1688641 1688642 1688643 1688644 1688645 1688646 1688647 1688648 1688649 ... ..$ : int [1:25091] 1732287 1732288 1732289 1732290 1732291 1732292 1732293 1732294 1732295 1732296 ... ..$ : int [1:24405] 1757378 1757379 1757380 1757381 1757382 1757383 1757384 1757385 1757386 1757387 ... ..$ : int [1:87102] 1781783 1781784 1781785 1781786 1781787 1781788 1781789 1781790 1781791 1781792 ... ..$ : int [1:8944] 1868885 1868886 1868887 1868888 1868889 1868890 1868891 1868892 1868893 1868894 ... ..$ : int [1:248] 1877829 1877830 1877831 1877832 1877833 1877834 1877835 1877836 1877837 1877838 ... ..$ : int [1:411] 1878077 1878078 1878079 1878080 1878081 1878082 1878083 1878084 1878085 1878086 ... $ chrs : int [1:25] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ gender : chr [1:228] "XX" "XX" "XX" "XX" ... $ sexchromosomes : chr [1:2] "23" "24"

str(gg) List of 2 $ germlinegenotypes: logi [1:1838128, 1:228] NA NA NA NA NA NA ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:1838128] "CN_473963" "CN_473964" "CN_473965" "CN_477984" ... .. ..$ : chr [1:228] "A1701-01,log2ratio,total" "A1701-02,log2ratio,total" "A1701-03,log2ratio,total" "A1701-05,log2ratio,total" ... $ failedarrays : NULL

name: OncotestMolecularCompendium_v1.6

tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

fullName: OncotestMolecularCompendium_v1.6,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2

nbrOfFiles: 228

srcFiles: A1701-01,fracB.asb A1701-02,fracB.asb A1701-03,fracB.asb A1701-05,fracB.asb A1701-09,fracB.asb A1701-11,fracB.asb A1701-14,fracB.asb A1701-16,fracB.asb A1701-17,fracB.asb A1701-18,fracB.asb A1701-19,fracB.asb A1701-21,fracB.asb A1701-22,fracB.asb A1701-26,fracB.asb A1701-27,fracB.asb A1701-30,fracB.asb A1801-01,fracB.asb A1801-02,fracB.asb A1801-04,fracB.asb A1801-05,fracB.asb A1801-06,fracB.asb A1801-07,fracB.asb A1801-09,fracB.asb A1801-10,fracB.asb A1801-12,fracB.asb A1801-15,fracB.asb A1801-17,fracB.asb A1801-18,fracB.asb A1801-19,fracB.asb A1801-20,fracB.asb A1801-22,fracB.asb A1801-23,fracB.asb A1801-24,fracB.asb A1801-25,fracB.asb A1801-27,fracB.asb A1801-31,fracB.asb A1801-32,fracB.asb A1801-34,fracB.asb A1801-36,fracB.asb A1801-38,fracB.asb A1955-004,fracB.asb A1955-006rh,fracB.asb A1955-007,fracB.asb A1955-008,fracB.asb A1955-009,fracB.asb A1955-010,fracB.asb A1955-013,fracB.asb A1955-014,fracB.asb A1955-016,fracB.asb A1955-017,fracB.asb A1955-018,fracB.asb A1955-020,fracB.asb A1955-021rh,fracB.asb A1955-022rh,fracB.asb A1955-033,fracB.asb A1955-034,fracB.asb A1955-035,fracB.asb A1955-036,fracB.asb A1955-038,fracB.asb A1955-039,fracB.asb A1955-040,fracB.asb A1955-041,fracB.asb A1955-045,fracB.asb A1955-048,fracB.asb A1955-049,fracB.asb A1955-063,fracB.asb A1955-066,fracB.asb A1955-067,fracB.asb A1955-068,fracB.asb A1955-070,fracB.asb A1955-072,fracB.asb A1955-073,fracB.asb A1955-075,fracB.asb A1955-076,fracB.asb A1955-082,fracB.asb A1955-087,fracB.asb A1955-088,fracB.asb A1955-090,fracB.asb A1955-091,fracB.asb A1955-092,fracB.asb A1955-094,fracB.asb A1955-100rh,fracB.asb A1955-107,fracB.asb A1955-113,fracB.asb A1955-115,fracB.asb A1955-117,fracB.asb A1955-119,fracB.asb A1955-122,fracB.asb A1955-124,fracB.asb A1955-127,fracB.asb A1955-128,fracB.asb A1955-130,fracB.asb A1955-132,fracB.asb A1955-136,fracB.asb A1955-138,fracB.asb A1955-139,fracB.asb A1955-145,fracB.asb A1955-147,fracB.asb AXF_984-1266,fracB.asb BXF_1258-9749,fracB.asb CEXF_633-6901,fracB.asb CNXF_498-2524,fracB.asb CXF_1034-4446,fracB.asb CXF_1086-7881,fracB.asb CXF_1096-1670,fracB.asb CXF_1103-4309,fracB.asb CXF_1297-3644,fracB.asb CXF_158-7553,fracB.asb CXF_1729-2517,fracB.asb CXF_1783-1853,fracB.asb CXF_1784-1174,fracB.asb CXF_1788-8837,fracB.asb CXF_2032-8080,fracB.asb CXF_233-2685,fracB.asb CXF_243-3450,fracB.asb CXF_260-8231,fracB.asb CXF_280-9681,fracB.asb CXF_533-7067,fracB.asb CXF_609-1110,fracB.asb CXF_676-8129,fracB.asb CXF_742-5370,fracB.asb CXF_975-3337,fracB.asb GXA_3002-5334,fracB.asb GXA_3011-8301,fracB.asb GXA_3013-1329,fracB.asb GXA_3027-4018,fracB.asb GXF_251-6477,fracB.asb GXF_281-3183,fracB.asb GXF_602-7914,fracB.asb GXF_97-9609,fracB.asb HNXF_536-3784,fracB.asb HNXF_908-7504,fracB.asb LXFA_1012-1139,fracB.asb LXFA_1041-2201,fracB.asb LXFA_1584-4190,fracB.asb LXFA_1647-3238,fracB.asb LXFA_1848-9907,fracB.asb LXFA_289-7251,fracB.asb LXFA_297-7167,fracB.asb LXFA_400-9946,fracB.asb LXFA_526-8219,fracB.asb LXFA_586-6508,fracB.asb LXFA_592-2222,fracB.asb LXFA_623-9345,fracB.asb LXFA_629-2652,fracB.asb LXFA_677-9758,fracB.asb LXFA_749-7793,fracB.asb LXFA_923-7874,fracB.asb LXFA_983-1825,fracB.asb LXFE_1022-1122,fracB.asb LXFE_1066-4986,fracB.asb LXFE_1422-8942,fracB.asb LXFE_211-5131,fracB.asb LXFE_397-1638,fracB.asb LXFE_409-8620,fracB.asb LXFE_470-6838,fracB.asb LXFE_597-4073,fracB.asb LXFE_646-7352,fracB.asb LXFE_690-2150,fracB.asb LXFE_937-5841,fracB.asb LXFL_1072-7634,fracB.asb LXFL_1121-2152,fracB.asb LXFL_1176-9949,fracB.asb LXFL_1674-2911,fracB.asb LXFL_430-2926,fracB.asb LXFL_529-6810,fracB.asb LXFL_625-2241,fracB.asb LXFS_538-3743,fracB.asb LXFS_573-1328,fracB.asb LXFS_615-5739,fracB.asb LXFS_650-9857,fracB.asb MAXF_1162-1406,fracB.asb MAXF_1322-1230,fracB.asb MAXF_1384-9459,fracB.asb MAXF_1398-4862,fracB.asb MAXF_401-9808,fracB.asb MAXF_449-8651,fracB.asb MAXF_508-1777,fracB.asb MAXF_574-4244,fracB.asb MAXF_583-3098,fracB.asb MAXF_857-3184,fracB.asb MAXF_MX1-9711,fracB.asb MEXF_1341-6216,fracB.asb MEXF_1732-7987,fracB.asb MEXF_1765-2371,fracB.asb MEXF_1792-1094,fracB.asb MEXF_1829-9933,fracB.asb MEXF_274-5165,fracB.asb MEXF_276-7909,fracB.asb MEXF_462-6609,fracB.asb MEXF_514-9135,fracB.asb MEXF_622-8283,fracB.asb MEXF_666-3786,fracB.asb MEXF_672-1172,fracB.asb MEXF_989-3233,fracB.asb OVXF_1023-5712,fracB.asb OVXF_1544-9842,fracB.asb OVXF_550-4338,fracB.asb PAXF_1657-3882,fracB.asb PAXF_1876-9329,fracB.asb PAXF_1881-8255,fracB.asb PAXF_1900-9520,fracB.asb PAXF_1965-7495,fracB.asb PAXF_1997-4821,fracB.asb PAXF_2005-5076,fracB.asb PAXF_2007-5736,fracB.asb PAXF_546-9483,fracB.asb PAXF_736-9196,fracB.asb PXF_1118-7709,fracB.asb PXF_1752-9309,fracB.asb PXF_537-1776,fracB.asb PXF_541-3557,fracB.asb PXF_698-8077,fracB.asb RXF_1003-2005,fracB.asb RXF_1183-3134,fracB.asb RXF_1220-2600,fracB.asb RXF_1393-1995,fracB.asb RXF_393-9789,fracB.asb RXF_423-8374,fracB.asb RXF_739-7683,fracB.asb SXF_117-6806,fracB.asb SXF_1186-5409,fracB.asb SXF_1301-1660,fracB.asb SXF_463-8354,fracB.asb SXF_627-8318,fracB.asb SXF_678-9969,fracB.asb TXF_593-9924,fracB.asb TXF_881-8658,fracB.asb

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names: A1701-01 A1701-02 A1701-03 A1701-05 A1701-09 A1701-11 A1701-14 A1701-16 A1701-17 A1701-18 A1701-19 A1701-21 A1701-22 A1701-26 A1701-27 A1701-30 A1801-01 A1801-02 A1801-04 A1801-05 A1801-06 A1801-07 A1801-09 A1801-10 A1801-12 A1801-15 A1801-17 A1801-18 A1801-19 A1801-20 A1801-22 A1801-23 A1801-24 A1801-25 A1801-27 A1801-31 A1801-32 A1801-34 A1801-36 A1801-38 A1955-004 A1955-006rh A1955-007 A1955-008 A1955-009 A1955-010 A1955-013 A1955-014 A1955-016 A1955-017 A1955-018 A1955-020 A1955-021rh A1955-022rh A1955-033 A1955-034 A1955-035 A1955-036 A1955-038 A1955-039 A1955-040 A1955-041 A1955-045 A1955-048 A1955-049 A1955-063 A1955-066 A1955-067 A1955-068 A1955-070 A1955-072 A1955-073 A1955-075 A1955-076 A1955-082 A1955-087 A1955-088 A1955-090 A1955-091 A1955-092 A1955-094 A1955-100rh A1955-107 A1955-113 A1955-115 A1955-117 A1955-119 A1955-122 A1955-124 A1955-127 A1955-128 A1955-130 A1955-132 A1955-136 A1955-138 A1955-139 A1955-145 A1955-147 AXF_984-1266 BXF_1258-9749 CEXF_633-6901 CNXF_498-2524 CXF_1034-4446 CXF_1086-7881 CXF_1096-1670 CXF_1103-4309 CXF_1297-3644 CXF_158-7553 CXF_1729-2517 CXF_1783-1853 CXF_1784-1174 CXF_1788-8837 CXF_2032-8080 CXF_233-2685 CXF_243-3450 CXF_260-8231 CXF_280-9681 CXF_533-7067 CXF_609-1110 CXF_676-8129 CXF_742-5370 CXF_975-3337 GXA_3002-5334 GXA_3011-8301 GXA_3013-1329 GXA_3027-4018 GXF_251-6477 GXF_281-3183 GXF_602-7914 GXF_97-9609 HNXF_536-3784 HNXF_908-7504 LXFA_1012-1139 LXFA_1041-2201 LXFA_1584-4190 LXFA_1647-3238 LXFA_1848-9907 LXFA_289-7251 LXFA_297-7167 LXFA_400-9946 LXFA_526-8219 LXFA_586-6508 LXFA_592-2222 LXFA_623-9345 LXFA_629-2652 LXFA_677-9758 LXFA_749-7793 LXFA_923-7874 LXFA_983-1825 LXFE_1022-1122 LXFE_1066-4986 LXFE_1422-8942 LXFE_211-5131 LXFE_397-1638 LXFE_409-8620 LXFE_470-6838 LXFE_597-4073 LXFE_646-7352 LXFE_690-2150 LXFE_937-5841 LXFL_1072-7634 LXFL_1121-2152 LXFL_1176-9949 LXFL_1674-2911 LXFL_430-2926 LXFL_529-6810 LXFL_625-2241 LXFS_538-3743 LXFS_573-1328 LXFS_615-5739 LXFS_650-9857 MAXF_1162-1406 MAXF_1322-1230 MAXF_1384-9459 MAXF_1398-4862 MAXF_401-9808 MAXF_449-8651 MAXF_508-1777 MAXF_574-4244 MAXF_583-3098 MAXF_857-3184 MAXF_MX1-9711 MEXF_1341-6216 MEXF_1732-7987 MEXF_1765-2371 MEXF_1792-1094 MEXF_1829-9933 MEXF_274-5165 MEXF_276-7909 MEXF_462-6609 MEXF_514-9135 MEXF_622-8283 MEXF_666-3786 MEXF_672-1172 MEXF_989-3233 OVXF_1023-5712 OVXF_1544-9842 OVXF_550-4338 PAXF_1657-3882 PAXF_1876-9329 PAXF_1881-8255 PAXF_1900-9520 PAXF_1965-7495 PAXF_1997-4821 PAXF_2005-5076 PAXF_2007-5736 PAXF_546-9483 PAXF_736-9196 PXF_1118-7709 PXF_1752-9309 PXF_537-1776 PXF_541-3557 PXF_698-8077 RXF_1003-2005 RXF_1183-3134 RXF_1220-2600 RXF_1393-1995 RXF_393-9789 RXF_423-8374 RXF_739-7683 SXF_117-6806 SXF_1186-5409 SXF_1301-1660 SXF_463-8354 SXF_627-8318 SXF_678-9969 TXF_593-9924 TXF_881-8658

tags: fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB fracB

fullNames: A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

platform: Affymetrix

chipType: GenomeWideSNP_6,Full

nbrOfUnits: 1881415

createdOn: 2016-04-11 16:03:43 CEST

createdBy: aroma.core v3.0.0

columnTypes: character numeric numeric double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double double

columnNames: unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB

unitName chromosome position A1701-01,fracB A1701-02,fracB A1701-03,fracB A1701-05,fracB A1701-09,fracB A1701-11,fracB A1701-14,fracB A1701-16,fracB A1701-17,fracB A1701-18,fracB A1701-19,fracB A1701-21,fracB A1701-22,fracB A1701-26,fracB A1701-27,fracB A1701-30,fracB A1801-01,fracB A1801-02,fracB A1801-04,fracB A1801-05,fracB A1801-06,fracB A1801-07,fracB A1801-09,fracB A1801-10,fracB A1801-12,fracB A1801-15,fracB A1801-17,fracB A1801-18,fracB A1801-19,fracB A1801-20,fracB A1801-22,fracB A1801-23,fracB A1801-24,fracB A1801-25,fracB A1801-27,fracB A1801-31,fracB A1801-32,fracB A1801-34,fracB A1801-36,fracB A1801-38,fracB A1955-004,fracB A1955-006rh,fracB A1955-007,fracB A1955-008,fracB A1955-009,fracB A1955-010,fracB A1955-013,fracB A1955-014,fracB A1955-016,fracB A1955-017,fracB A1955-018,fracB A1955-020,fracB A1955-021rh,fracB A1955-022rh,fracB A1955-033,fracB A1955-034,fracB A1955-035,fracB A1955-036,fracB A1955-038,fracB A1955-039,fracB A1955-040,fracB A1955-041,fracB A1955-045,fracB A1955-048,fracB A1955-049,fracB A1955-063,fracB A1955-066,fracB A1955-067,fracB A1955-068,fracB A1955-070,fracB A1955-072,fracB A1955-073,fracB A1955-075,fracB A1955-076,fracB A1955-082,fracB A1955-087,fracB A1955-088,fracB A1955-090,fracB A1955-091,fracB A1955-092,fracB A1955-094,fracB A1955-100rh,fracB A1955-107,fracB A1955-113,fracB A1955-115,fracB A1955-117,fracB A1955-119,fracB A1955-122,fracB A1955-124,fracB A1955-127,fracB A1955-128,fracB A1955-130,fracB A1955-132,fracB A1955-136,fracB A1955-138,fracB A1955-139,fracB A1955-145,fracB A1955-147,fracB AXF_984-1266,fracB BXF_1258-9749,fracB CEXF_633-6901,fracB CNXF_498-2524,fracB CXF_1034-4446,fracB CXF_1086-7881,fracB CXF_1096-1670,fracB CXF_1103-4309,fracB CXF_1297-3644,fracB CXF_158-7553,fracB CXF_1729-2517,fracB CXF_1783-1853,fracB CXF_1784-1174,fracB CXF_1788-8837,fracB CXF_2032-8080,fracB CXF_233-2685,fracB CXF_243-3450,fracB CXF_260-8231,fracB CXF_280-9681,fracB CXF_533-7067,fracB CXF_609-1110,fracB CXF_676-8129,fracB CXF_742-5370,fracB CXF_975-3337,fracB GXA_3002-5334,fracB GXA_3011-8301,fracB GXA_3013-1329,fracB GXA_3027-4018,fracB GXF_251-6477,fracB GXF_281-3183,fracB GXF_602-7914,fracB GXF_97-9609,fracB HNXF_536-3784,fracB HNXF_908-7504,fracB LXFA_1012-1139,fracB LXFA_1041-2201,fracB LXFA_1584-4190,fracB LXFA_1647-3238,fracB LXFA_1848-9907,fracB LXFA_289-7251,fracB LXFA_297-7167,fracB LXFA_400-9946,fracB LXFA_526-8219,fracB LXFA_586-6508,fracB LXFA_592-2222,fracB LXFA_623-9345,fracB LXFA_629-2652,fracB LXFA_677-9758,fracB LXFA_749-7793,fracB LXFA_923-7874,fracB LXFA_983-1825,fracB LXFE_1022-1122,fracB LXFE_1066-4986,fracB LXFE_1422-8942,fracB LXFE_211-5131,fracB LXFE_397-1638,fracB LXFE_409-8620,fracB LXFE_470-6838,fracB LXFE_597-4073,fracB LXFE_646-7352,fracB LXFE_690-2150,fracB LXFE_937-5841,fracB LXFL_1072-7634,fracB LXFL_1121-2152,fracB LXFL_1176-9949,fracB LXFL_1674-2911,fracB LXFL_430-2926,fracB LXFL_529-6810,fracB LXFL_625-2241,fracB LXFS_538-3743,fracB LXFS_573-1328,fracB LXFS_615-5739,fracB LXFS_650-9857,fracB MAXF_1162-1406,fracB MAXF_1322-1230,fracB MAXF_1384-9459,fracB MAXF_1398-4862,fracB MAXF_401-9808,fracB MAXF_449-8651,fracB MAXF_508-1777,fracB MAXF_574-4244,fracB MAXF_583-3098,fracB MAXF_857-3184,fracB MAXF_MX1-9711,fracB MEXF_1341-6216,fracB MEXF_1732-7987,fracB MEXF_1765-2371,fracB MEXF_1792-1094,fracB MEXF_1829-9933,fracB MEXF_274-5165,fracB MEXF_276-7909,fracB MEXF_462-6609,fracB MEXF_514-9135,fracB MEXF_622-8283,fracB MEXF_666-3786,fracB MEXF_672-1172,fracB MEXF_989-3233,fracB OVXF_1023-5712,fracB OVXF_1544-9842,fracB OVXF_550-4338,fracB PAXF_1657-3882,fracB PAXF_1876-9329,fracB PAXF_1881-8255,fracB PAXF_1900-9520,fracB PAXF_1965-7495,fracB PAXF_1997-4821,fracB PAXF_2005-5076,fracB PAXF_2007-5736,fracB PAXF_546-9483,fracB PAXF_736-9196,fracB PXF_1118-7709,fracB PXF_1752-9309,fracB PXF_537-1776,fracB PXF_541-3557,fracB PXF_698-8077,fracB RXF_1003-2005,fracB RXF_1183-3134,fracB RXF_1220-2600,fracB RXF_1393-1995,fracB RXF_393-9789,fracB RXF_423-8374,fracB RXF_739-7683,fracB SXF_117-6806,fracB SXF_1186-5409,fracB SXF_1301-1660,fracB SXF_463-8354,fracB SXF_627-8318,fracB SXF_678-9969,fracB TXF_593-9924,fracB TXF_881-8658,fracB AFFX-5Q-123 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

[haasek]

Hi Thomas,

good news, I found the issue that caused your segmentation to fail with the help of your example data. The problem was that many of the probes in your set were not part of our standard SNP6 set and are hence not cover by the GC correction. I made a few changes to the GC correction function and it resolved the problem on my end. Please try ASCAT's latest release 2.4.2 and let me know if that also works for you.

Best wishes, Kerstin

[ThomasGro]

Hi Kerstin,

That is good news. I will give it a try beginning of next week.

Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:08 An: Crick-CancerGenomics/ascat ascat@noreply.github.com Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com; Author author@noreply.github.com Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

good news, I found the issue that caused your segmentation to fail with the help of your example data. The problem was that many of the probes in your set were not part of our standard SNP6 set and are hence not cover by the GC correction. I made a few changes to the GC correction function and it resolved the problem on my end. Please try ASCAT's latest release 2.4.2 and let me know if that also works for you.

Best wishes, Kerstin

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213442155

This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith.

Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

[ThomasGro]

Dear Kerstin,

One question to this: do I need and do you also provide a new GC_AffySNP6 file for GC correction? Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:08 An: Crick-CancerGenomics/ascat ascat@noreply.github.com Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com; Author author@noreply.github.com Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

good news, I found the issue that caused your segmentation to fail with the help of your example data. The problem was that many of the probes in your set were not part of our standard SNP6 set and are hence not cover by the GC correction. I made a few changes to the GC correction function and it resolved the problem on my end. Please try ASCAT's latest release 2.4.2 and let me know if that also works for you.

Best wishes, Kerstin

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213442155

This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith.

Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

[haasek]

Hi Thomas,

no, the one you have is completely fine. The problem was internal and not from the input.

Best wishes, Kerstin

On 22 Apr 2016, at 15:39, ThomasGro notifications@github.com<mailto:notifications@github.com> wrote:

Dear Kerstin,

One question to this: do I need and do you also provide a new GC_AffySNP6 file for GC correction? Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:08 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com>; Author author@noreply.github.com<mailto:author@noreply.github.com> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

good news, I found the issue that caused your segmentation to fail with the help of your example data. The problem was that many of the probes in your set were not part of our standard SNP6 set and are hence not cover by the GC correction. I made a few changes to the GC correction function and it resolved the problem on my end. Please try ASCAT's latest release 2.4.2 and let me know if that also works for you.

Best wishes, Kerstin

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213442155

This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith.

Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

— You are receiving this because you commented. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213452302

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

[ThomasGro]

Dear Kerstin, I want to give you an update on the 2.4.2. release: my samples are not finished with the pipeline, but the segmentation seems to work now, with this new release. Thank you for your support. Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:45 An: Crick-CancerGenomics/ascat ascat@noreply.github.com Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com; Author author@noreply.github.com Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

no, the one you have is completely fine. The problem was internal and not from the input.

Best wishes, Kerstin

On 22 Apr 2016, at 15:39, ThomasGro notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

Dear Kerstin,

One question to this: do I need and do you also provide a new GC_AffySNP6 file for GC correction? Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:08 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com<mailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

good news, I found the issue that caused your segmentation to fail with the help of your example data. The problem was that many of the probes in your set were not part of our standard SNP6 set and are hence not cover by the GC correction. I made a few changes to the GC correction function and it resolved the problem on my end. Please try ASCAT's latest release 2.4.2 and let me know if that also works for you.

Best wishes, Kerstin

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213442155

This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith.

Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

— You are receiving this because you commented. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213452302

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/Crick-CancerGenomics/ascat/issues/4#issuecomment-213455214

This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith.

Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

[haasek]

Dear Thomas,

thank you for your update. I’m happy to hear that it solved your problem.

Best wishes, Kerstin

On 27 Apr 2016, at 10:34, ThomasGro notifications@github.com<mailto:notifications@github.com> wrote:

Dear Kerstin, I want to give you an update on the 2.4.2. release: my samples are not finished with the pipeline, but the segmentation seems to work now, with this new release. Thank you for your support. Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:45 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.com> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.com>; Author author@noreply.github.com<mailto:author@noreply.github.com> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

no, the one you have is completely fine. The problem was internal and not from the input.

Best wishes, Kerstin

On 22 Apr 2016, at 15:39, ThomasGro notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com%3cmailto:notifications@github.com<http://github.com>> wrote:

Dear Kerstin,

One question to this: do I need and do you also provide a new GC_AffySNP6 file for GC correction? Best, Thomas Von: haasek [mailto:notifications@github.com] Gesendet: Freitag, 22. April 2016 16:08 An: Crick-CancerGenomics/ascat ascat@noreply.github.com<mailto:ascat@noreply.github.commailto:ascat@noreply.github.commailto:ascat@noreply.github.com%3cmailto:ascat@noreply.github.com<http://noreply.github.com>> Cc: Thomas Grombacher Thomas.Grombacher@merckgroup.com<mailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.commailto:Thomas.Grombacher@merckgroup.com%3cmailto:Thomas.Grombacher@merckgroup.com<http://merckgroup.com>>; Author author@noreply.github.com<mailto:author@noreply.github.commailto:author@noreply.github.commailto:author@noreply.github.com%3cmailto:author@noreply.github.com<http://noreply.github.com>> Betreff: Re: [Crick-CancerGenomics/ascat] ascat.aspcf failed for tumor only data (#4)

Hi Thomas,

good news, I found the issue that caused your segmentation to fail with the help of your example data. The problem was that many of the probes in your set were not part of our standard SNP6 set and are hence not cover by the GC correction. I made a few changes to the GC correction function and it resolved the problem on my end. Please try ASCAT's latest release 2.4.2 and let me know if that also works for you.

Best wishes, Kerstin

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