Purity ratio

[solivehong]

After the previous problem was found that the purity of the VCF was not caused by NA, after testing our sample can be normal operation, but the purity is NA, whether there is a minimum purity or can change the parameters?

[solivehong]

$emflags [1] " Noisy sample, Calls can be unreliable."

[Elise-Merritt]

I am also getting the value NA for purity. Is this related to the warning message In max(mafR.clust[seg$chrom < nX & seg$nhet > min.nhet], na.rm = T) : no non-missing arguments to max; returning -Inf or is it caused by something else, and is there a way to still get the purity? The code I'm trying to use is below.

library(pctGCdata) library(facets) rcmat=readSnpMatrix("Xia-03_BQSRed.bam.RC") xx=preProcSample(rcmat, gbuild="mm10", ndepth=8) oo=procSample(xx, cval=150) oo$dipLogR [1] -0.01212792 fit=emcncf(oo) Warning message: In max(mafR.clust[seg$chrom < nX & seg$nhet > min.nhet], na.rm = T) : no non-missing arguments to max; returning -Inf fit$purity [1] NA fit$ploidy [1] 2 plotSample(x=oo, emfit=fit) fit2=emcncf2(oo) Warning messages: 1: 'emcncf2' is deprecated. Use 'emcncf' instead. See help("Deprecated") 2: In emcncf2(oo) : emcncf2 occationally returns quirky copy number estimates due to the clonal cluster structure imposed. please use with caution. 3: In max(mafR.clust[seg$chrom < nX & seg$nhet > 15], na.rm = T) : no non-missing arguments to max; returning -Inf

I've attached the data I'm working with. Xia-03_BQSRed.bam.RC.txt

[veseshan]

@zhaohongqiangsoliva - You have not provided any information that can be used. The best guess is that your sample is too noisy or has no discernible copy number changes.

@Elise-Merritt Your sample has no het SNPs

> table(xx$pmat$het)

   0 
7805 

Facets needs het SNPs to be able to estimate allele specific copy numbers and purity.

[solivehong]

chrom seg num.mark nhet cnlr.median mafR segclust cnlr.median.clust 1 1 1 854 69 0.069820928 0.264180863 15 0.053275452 2 2 2 900 64 -0.127231098 0.094425322 12 -0.121125389 3 3 3 898 74 0.120592805 0.318227265 18 0.136740489 4 4 4 78 7 0.377693682 0.067534256 23 0.377693682 5 4 5 12 0 -2.518024953 0.000000000 1 -2.518024953 6 4 6 437 37 -0.909902570 0.145011119 3 -0.909902570 7 5 7 466 40 -0.262245402 0.985859273 9 -0.273210780 8 5 8 26 0 -2.389390549 0.000000000 2 -2.389390549 9 5 9 109 14 -0.244019998 1.151891138 10 -0.273210780 10 6 10 617 70 0.063197294 0.105924472 15 0.053275452 11 7 11 975 87 0.268269728 0.008630779 20 0.263339911 12 8 12 402 30 0.339838406 0.140957832 22 0.322425495 13 9 13 384 24 -0.058914361 0.429879354 13 -0.064312984 14 10 14 479 47 0.035671790 0.459593218 16 0.053275452 15 11 15 591 48 -0.289157062 0.429998985 7 -0.273210780 16 12 16 876 95 -0.008845532 1.286489922 14 -0.008845532 17 12 17 131 38 0.572853926 0.124168041 25 0.572853926 18 13 18 361 55 -0.110942677 0.362860661 12 -0.121125389 19 14 19 271 20 0.315698285 0.053802713 22 0.322425495 20 15 20 40 4 -0.625163129 0.303708339 5 -0.625163129 21 15 21 292 24 0.490975168 1.124466557 24 0.490975168 22 15 22 294 40 -0.521271092 1.041692585 6 -0.521271092 23 16 23 650 40 -0.066190568 0.210637081 13 -0.064312984 24 17 24 875 73 0.255362721 0.448950391 21 0.263339911 25 18 25 154 10 -0.675857354 0.027691880 4 -0.675857354 26 19 26 419 42 -0.280257008 1.435696073 8 -0.273210780 27 19 27 200 15 0.144665792 0.142180795 18 0.136740489 28 20 28 222 16 0.187188211 0.180152091 19 0.187188211 29 21 29 135 5 0.049486146 0.091142853 17 0.053275452 30 22 30 707 74 -0.186068447 1.151547145 11 -0.186068447 31 23 31 377 0 0.038649312 0.000000000 17 0.053275452 mafR.clust start end cf.em tcn.em lcn.em purity ploidy 1 0.201270591 2488153 244006415 0.4429349 3 1 0.4429349 2.941422 2 0.216101135 173315 234680955 0.2200301 3 0 0.4429349 2.941422 3 0.281894561 3192669 197350997 0.4429349 3 1 0.4429349 2.941422 4 NA 1725007 8176700 0.3801015 5 NA 0.4429349 2.941422 5 NA 10256980 25664348 0.4429349 0 0 0.4429349 2.941422 6 0.145011119 25665677 190396161 0.3568139 0 0 0.4429349 2.941422 7 0.985859273 42780 149792109 0.4429349 2 0 0.4429349 2.941422 8 NA 156607843 156679841 0.4429349 0 0 0.4429349 2.941422 9 NA 170814899 180527499 NA 2 NA 0.4429349 2.941422 10 0.201270591 394711 168370528 0.4429349 3 1 0.4429349 2.941422 11 0.008630779 2946341 152132812 0.4429349 4 2 0.4429349 2.941422 12 0.112261123 18079517 145892243 0.3071983 6 2 0.4429349 2.941422 13 0.274803962 5021879 139438698 0.3129297 3 0 0.4429349 2.941422 14 0.459593218 8097561 131564998 0.2387479 4 0 0.4429349 2.941422 15 0.429998985 532803 128786515 0.3166070 2 0 0.4429349 2.941422 16 1.286489922 401880 121431225 0.4235519 3 0 0.4429349 2.941422 17 0.124168041 121431575 133263957 0.4429349 6 2 0.4429349 2.941422 18 0.216101135 19923357 113917748 0.2200301 3 0 0.4429349 2.941422 19 0.112261123 19487495 105263608 0.3071983 6 2 0.4429349 2.941422 20 NA 20488634 22151876 0.4329539 1 0 0.4429349 2.941422 21 1.124466557 23285530 50774134 0.4429349 5 1 0.4429349 2.941422 22 1.041692585 50782207 99500806 0.4429349 1 0 0.4429349 2.941422 23 0.274803962 338114 90241702 0.3129297 3 0 0.4429349 2.941422 24 0.448950391 591078 78938085 0.4429349 4 1 0.4429349 2.941422 25 NA 116884 77208837 0.4429349 1 0 0.4429349 2.941422 26 1.435696073 1206786 20101738 0.4429349 2 0 0.4429349 2.941422 27 0.281894561 30303714 54618843 0.4429349 3 1 0.4429349 2.941422 28 0.180152091 4040666 62922670 0.4429349 4 1 0.4429349 2.941422 29 NA 10996089 44524648 0.4429349 3 NA 0.4429349 2.941422 30 1.151547145 16347845 47755894 0.4429349 2 0 0.4429349 2.941422 31 NA 1314837 152845573 0.4429349 2 NA 0.4429349 2.941422 loglik 1 205.2223 2 205.2223 3 205.2223 4 205.2223 5 205.2223 6 205.2223 7 205.2223 8 205.2223 9 205.2223 10 205.2223 11 205.2223 12 205.2223 13 205.2223 14 205.2223 15 205.2223 16 205.2223 17 205.2223 18 205.2223 19 205.2223 20 205.2223 21 205.2223 22 205.2223 23 205.2223 24 205.2223 25 205.2223 26 205.2223 27 205.2223 28 205.2223 29 205.2223 30 205.2223 31 205.2223 I have already arrived at the result, but I want to know what exactly determines the purity of the NA,

[solivehong]

Thanks for your quick answer。 I summed up what I wanted to know A fragment trusted threshold parameter， LOH minimum trusted segment length, The lowest tumor detection line，