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ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://shixiangwang.github.io/sigminer/
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Row names discrepancy for latest_CN_GRCh37CNS_TCGA #421

Closed dnousome closed 1 year ago

dnousome commented 1 year ago

Hi,

Thank you for a great package.

The latest_CN_GRCh37 row names do not match the CNS_TCGA row names and the sig_tally will look different between the two. Looks like the difference is between Kb/kb in these row names.

ShixiangWang commented 1 year ago

@dnousome Thanks for your reporting and it's possible to see this. I will take a look and see if I can take a quick fix in github version.

ShixiangWang commented 1 year ago

@dnousome A quick fix has been made in Github latest commit. Reinstalling the package from Github shall work now. Thanks again for your bug report :).

> x = get_sig_db("latest_CN_GRCh37")
The data is not available in local, obtain it from COSMIC: https://cancer.sanger.ac.uk/signatures/downloads/
Transforming and saving to D:/Repos/sigminer/inst/extdata/COSMIC_v3.3_CN_GRCh37.rds
> x$db
                              CN1            CN2        CN3        CN4         CN5          CN6
0:homdel:0-100Kb   0.001795053890 0.002237674329 0.06404424 0.00096628 0.025822490 0.0034924998
0:homdel:100Kb-1Mb 0.003807103951 0.007195787621 0.00640384 0.00021955 0.024993570 0.0075503095
0:homdel:>1Mb      0.002436746098 0.003837108012 0.01303343 0.00006124 0.003888700 0.0013361699
1:LOH:0-100Kb      0.002840449153 0.002826535986 0.06221358 0.05615077 0.015829115 0.0059558296
1:LOH:100Kb-1Mb    0.012263056631 0.006323914617 0.01261482 0.24779892 0.026544940 0.0105207593
1:LOH:1Mb-10Mb     0.019163417893 0.001023763998 0.01928346 0.08336934 0.001358030 0.0009915099
1:LOH:10Mb-40Mb    0.047297757322 0.000483364338 0.00871990 0.00010096 0.000573685 0.0004099400
1:LOH:>40Mb        0.073645998516 0.000124321668 0.00409212 0.00230378 0.000080995 0.0001791700
2:LOH:0-100Kb      0.001187984350 0.002488916646 0.00138849 0.01414630 0.013351500 0.0192514487
2:LOH:100Kb-1Mb    0.004303101724 0.019464869185 0.03383514 0.04008938 0.255496412 0.1772921576
2:LOH:1Mb-10Mb     0.004438012587 0.033551542805 0.01899058 0.00618009 0.264575824 0.1163828519
2:LOH:10Mb-40Mb    0.004318590464 0.052291174730 0.00267497 0.00024516 0.067065891 0.0063248096
2:LOH:>40Mb        0.012215653566 0.067374759875 0.00008237 0.00241502 0.019616490 0.0002609300
3-4:LOH:0-100Kb    0.001379947395 0.002717402002 0.00271910 0.01402566 0.005480255 0.0050518296
3-4:LOH:100Kb-1Mb  0.001667853035 0.013819445054 0.02381122 0.01144021 0.026855770 0.0135102791
3-4:LOH:1Mb-10Mb   0.001514284347 0.012471389014 0.03436767 0.00010785 0.029519046 0.0040970397
3-4:LOH:10Mb-40Mb  0.000102202610 0.010631238635 0.02189155 0.00000010 0.004552090 0.0000560700
3-4:LOH:>40Mb      0.007367609159 0.017426922018 0.02529479 0.00000013 0.000735890 0.0003285500
5-8:LOH:0-100Kb    0.000351297826 0.001689411337 0.00000053 0.02552717 0.000664530 0.0004894900
5-8:LOH:100Kb-1Mb  0.000212106955 0.003416253020 0.00256956 0.00169273 0.000652505 0.0003104600
5-8:LOH:1Mb-10Mb   0.000207783479 0.004495305663 0.00554920 0.00000019 0.000278185 0.0002143500
5-8:LOH:10Mb-40Mb  0.000099715217 0.002756042327 0.00000071 0.00001314 0.000125705 0.0001177100
5-8:LOH:>40Mb      0.000331938261 0.010089624349 0.00535955 0.00000014 0.000098750 0.0003040600
9+:LOH:0-100Kb     0.000133994783 0.000520196003 0.00000071 0.00001056 0.001312595 0.0049314197
9+:LOH:100Kb-1Mb   0.000411987828 0.000668643002 0.00216196 0.00000028 0.003306250 0.0054595396
9+:LOH:1Mb-10Mb    0.000200770001 0.000828997325 0.00220660 0.00000028 0.000649225 0.0008671599
9+:LOH:10Mb-40Mb   0.000006514783 0.000350903003 0.00211290 0.00000028 0.000015135 0.0000126800
9+:LOH:>40Mb       0.000002757826 0.000712768005 0.00092755 0.00000028 0.000012310 0.0000340000
2:het:0-100Kb      0.000126855217 0.001077283324 0.02085150 0.00018321 0.001733870 0.0035613998
2:het:100Kb-1Mb    0.002392692165 0.001448574994 0.01137198 0.00093060 0.008359660 0.0018074599
2:het:1Mb-10Mb     0.017226427425 0.000571467668 0.02363235 0.00124271 0.047988820 0.0086287494
2:het:10Mb-40Mb    0.112043886286 0.000401269997 0.02432782 0.00653021 0.040189910 0.0089315194
2:het:>40Mb        0.647548237436 0.000001616667 0.02278876 0.04721082 0.000000615 0.0020075299
3-4:het:0-100Kb    0.000986436966 0.001301612661 0.01675940 0.02839772 0.004295095 0.0094994693
3-4:het:100Kb-1Mb  0.003623146982 0.015217479637 0.04264799 0.20328865 0.027386325 0.2055037256
3-4:het:1Mb-10Mb   0.001734587400 0.058156429853 0.02762061 0.05567599 0.015401125 0.2333349037
3-4:het:10Mb-40Mb  0.003009542199 0.135200883071 0.01850544 0.00340995 0.020384580 0.0629906556
3-4:het:>40Mb      0.005373924797 0.390284779081 0.00000018 0.00472731 0.002974155 0.0024052698
5-8:het:0-100Kb    0.000741211739 0.001717200662 0.00551728 0.06860624 0.003368305 0.0036253197
5-8:het:100Kb-1Mb  0.000116379998 0.011630411571 0.03952374 0.05686576 0.007209015 0.0045492397
5-8:het:1Mb-10Mb   0.000204002174 0.019335547908 0.16260339 0.01134511 0.008309545 0.0020514199
                          CN7         CN8            CN9       CN10       CN11       CN12       CN13
0:homdel:0-100Kb   0.00000000 0.000216260 0.008181841768 0.00779524 0.00161374 0.02309338 0.00224368
0:homdel:100Kb-1Mb 0.00000000 0.000720975 0.020999189073 0.03122532 0.00590270 0.05272477 0.03467842
0:homdel:>1Mb      0.00000000 0.000269340 0.009009219066 0.00455881 0.00313081 0.00686610 0.01814564
1:LOH:0-100Kb      0.00011082 0.000950405 0.018583651848 0.00879753 0.00275430 0.02182354 0.00284705
1:LOH:100Kb-1Mb    0.00504080 0.007283630 0.130807871527 0.03974523 0.00623170 0.06597701 0.02886982
1:LOH:1Mb-10Mb     0.00007442 0.002204905 0.159949199370 0.01091525 0.01775071 0.00423455 0.12860718
1:LOH:10Mb-40Mb    0.00000002 0.003664150 0.076229355119 0.00290428 0.00184154 0.00004033 0.15419780
1:LOH:>40Mb        0.00000000 0.006089315 0.027000692781 0.00148398 0.00005754 0.00000464 0.21568204
2:LOH:0-100Kb      0.00277607 0.011115840 0.004119057252 0.00635726 0.00148901 0.00590696 0.00005691
2:LOH:100Kb-1Mb    0.00454340 0.022282900 0.013774232673 0.08782354 0.01694496 0.08093648 0.02909678
2:LOH:1Mb-10Mb     0.00457336 0.008298320 0.011594392672 0.13191050 0.04392020 0.13267104 0.03957572
2:LOH:10Mb-40Mb    0.00004105 0.001159380 0.004945151804 0.08706983 0.02467614 0.17672789 0.01185966
2:LOH:>40Mb        0.00000000 0.000131970 0.002407304544 0.01593395 0.01121149 0.13622451 0.00008495
3-4:LOH:0-100Kb    0.00420447 0.009564720 0.001833529085 0.00743812 0.00158209 0.00930253 0.00057156
3-4:LOH:100Kb-1Mb  0.00232790 0.004662895 0.002848604541 0.06845530 0.04824190 0.03071852 0.00817896
3-4:LOH:1Mb-10Mb   0.00021573 0.003492150 0.003443509989 0.09646664 0.15626472 0.04005227 0.01705423
3-4:LOH:10Mb-40Mb  0.00000079 0.002194095 0.001390007273 0.04754809 0.05527416 0.02606018 0.00759605
3-4:LOH:>40Mb      0.00000674 0.003399115 0.001198600905 0.01319828 0.03509218 0.01659015 0.00381337
5-8:LOH:0-100Kb    0.00552275 0.010770475 0.000375937273 0.00260391 0.00501223 0.00578286 0.00294361
5-8:LOH:100Kb-1Mb  0.00682636 0.009675285 0.000836165454 0.02207809 0.04217432 0.00208666 0.00123595
5-8:LOH:1Mb-10Mb   0.00006776 0.002155840 0.000661617270 0.02022345 0.07357179 0.00322838 0.00610440
5-8:LOH:10Mb-40Mb  0.00000000 0.001022835 0.000376486361 0.00679665 0.01532663 0.00163617 0.00077852
5-8:LOH:>40Mb      0.00004933 0.001459620 0.000382634545 0.00017289 0.00347323 0.00110016 0.00162804
9+:LOH:0-100Kb     0.00632901 0.022043315 0.000759423640 0.00018531 0.00062013 0.00048688 0.00004453
9+:LOH:100Kb-1Mb   0.02139771 0.028381515 0.001234373638 0.00299660 0.01160088 0.00011188 0.00344403
9+:LOH:1Mb-10Mb    0.01464548 0.008094730 0.000574561822 0.00365022 0.02224864 0.00012019 0.00163639
9+:LOH:10Mb-40Mb   0.00000061 0.000025265 0.000010190000 0.00044558 0.00252885 0.00006139 0.00000061
9+:LOH:>40Mb       0.00000002 0.000111790 0.000004554545 0.00000009 0.00148788 0.00001647 0.00013687
2:het:0-100Kb      0.00021658 0.001038500 0.002813762724 0.00213926 0.00000000 0.00068448 0.00242738
2:het:100Kb-1Mb    0.00209292 0.000889200 0.057456734254 0.00460283 0.00000001 0.00313133 0.00710641
2:het:1Mb-10Mb     0.00016457 0.002329035 0.159920320844 0.00069290 0.00000000 0.00410482 0.06241927
2:het:10Mb-40Mb    0.00000000 0.002674940 0.129543643223 0.00078362 0.00000393 0.00107820 0.06807839
2:het:>40Mb        0.00000031 0.002161405 0.006767871088 0.00000006 0.00000008 0.00000043 0.06958505
3-4:het:0-100Kb    0.00362014 0.013551545 0.006686778158 0.00557084 0.00042229 0.00495000 0.00027983
3-4:het:100Kb-1Mb  0.06003456 0.041391180 0.067471317676 0.04177622 0.00000650 0.00936991 0.01942203
3-4:het:1Mb-10Mb   0.12143735 0.026193135 0.043510864271 0.08695636 0.01763335 0.01812126 0.02082491
3-4:het:10Mb-40Mb  0.00493032 0.004956070 0.007530375458 0.06757995 0.00761337 0.10067989 0.01275603
3-4:het:>40Mb      0.00022509 0.024168520 0.002876184608 0.00000001 0.00006203 0.00090365 0.00958487
5-8:het:0-100Kb    0.01467759 0.032617975 0.001719671803 0.00596208 0.00002945 0.00044794 0.00098094
5-8:het:100Kb-1Mb  0.16196039 0.127337371 0.001350210012 0.04005666 0.04380270 0.00783497 0.00090333
5-8:het:1Mb-10Mb   0.21136197 0.061241481 0.001136105468 0.01210908 0.18536884 0.00156351 0.00000058
                         CN14       CN15       CN16       CN17             CN18       CN19       CN20
0:homdel:0-100Kb   0.01214770 0.00674380 0.00366730 0.00136668 0.00110894007763 0.00591472 0.00004078
0:homdel:100Kb-1Mb 0.03389276 0.02652628 0.00109281 0.00143123 0.00303045021213 0.00677398 0.00017845
0:homdel:>1Mb      0.00000044 0.00524487 0.04053983 0.00145330 0.00075840005309 0.00411050 0.00011722
1:LOH:0-100Kb      0.00129939 0.00763888 0.00142666 0.00211427 0.00155560010889 0.01041569 0.00050182
1:LOH:100Kb-1Mb    0.01293743 0.00252662 0.00580905 0.00507205 0.00141876009931 0.06429375 0.00081924
1:LOH:1Mb-10Mb     0.00002022 0.00000010 0.00343106 0.01868840 0.00028103001967 0.03777062 0.00624116
1:LOH:10Mb-40Mb    0.00000014 0.00000044 0.00204512 0.00550295 0.00000008000001 0.02105378 0.00283775
1:LOH:>40Mb        0.00000187 0.00030730 0.00064424 0.00000134 0.00000165000012 0.00174097 0.00001202
2:LOH:0-100Kb      0.00762253 0.00228469 0.00067984 0.00055893 0.00273632019154 0.00566334 0.00060974
2:LOH:100Kb-1Mb    0.00707926 0.02151070 0.01758306 0.00062269 0.00655180045863 0.05489644 0.00134094
2:LOH:1Mb-10Mb     0.02585003 0.00886790 0.01162738 0.08444233 0.00018517001296 0.11706714 0.01443458
2:LOH:10Mb-40Mb    0.09336807 0.00201416 0.00291477 0.08848328 0.00015695001099 0.04188772 0.00966270
2:LOH:>40Mb        0.55221236 0.00000033 0.00170498 0.00750380 0.00007257000508 0.03389879 0.00049936
3-4:LOH:0-100Kb    0.00141835 0.00197133 0.00093853 0.00267395 0.00226406015848 0.01388264 0.00256100
3-4:LOH:100Kb-1Mb  0.00688559 0.01163685 0.02159759 0.02375527 0.01402709098190 0.01258572 0.02182453
3-4:LOH:1Mb-10Mb   0.00687404 0.04837325 0.04370100 0.09462731 0.05963823417468 0.00110793 0.02055562
3-4:LOH:10Mb-40Mb  0.00128688 0.16721937 0.03291840 0.05183615 0.07185141502960 0.00278047 0.00224340
3-4:LOH:>40Mb      0.00007351 0.37328855 0.19071235 0.00224311 0.05059881354192 0.00421117 0.00094554
5-8:LOH:0-100Kb    0.00316274 0.00348453 0.00347840 0.00128554 0.00482129033749 0.00002587 0.00091844
5-8:LOH:100Kb-1Mb  0.00000647 0.01942632 0.00980644 0.00726579 0.02136849149579 0.00000814 0.00241053
5-8:LOH:1Mb-10Mb   0.00000023 0.02016289 0.01073875 0.01836005 0.04681185327683 0.00001578 0.00524955
5-8:LOH:10Mb-40Mb  0.00000896 0.01347168 0.00622641 0.00502947 0.02208834154618 0.00068876 0.00029923
5-8:LOH:>40Mb      0.00572642 0.06422257 0.01067078 0.00000129 0.00536994037590 0.00012041 0.00012116
9+:LOH:0-100Kb     0.00000146 0.00300605 0.00384194 0.00012468 0.00241473016903 0.00107168 0.00014531
9+:LOH:100Kb-1Mb   0.00000085 0.00785032 0.00471630 0.00005302 0.01211638084815 0.00117826 0.00085741
9+:LOH:1Mb-10Mb    0.00001099 0.00480835 0.00000235 0.00001369 0.01534961107447 0.00000016 0.00046208
9+:LOH:10Mb-40Mb   0.00000159 0.00234481 0.00000235 0.00005292 0.00097940006856 0.00000016 0.00010940
9+:LOH:>40Mb       0.00000123 0.00380205 0.00333085 0.00000029 0.00000077000005 0.00004662 0.00001071
2:het:0-100Kb      0.00144658 0.00001035 0.00266672 0.00038608 0.00029759002083 0.00311810 0.00053199
2:het:100Kb-1Mb    0.00038720 0.00006600 0.00197375 0.00018880 0.00003020000211 0.03122830 0.00464189
2:het:1Mb-10Mb     0.00011283 0.00000117 0.00185384 0.00087384 0.00000011000001 0.01642660 0.00278654
2:het:10Mb-40Mb    0.00000103 0.00020074 0.00136271 0.00061789 0.00000034000002 0.00452687 0.00139670
2:het:>40Mb        0.00000246 0.00006456 0.00000075 0.00000000 0.00000032000002 0.00000046 0.00000815
3-4:het:0-100Kb    0.00058958 0.00008096 0.00179605 0.00015917 0.00117086008196 0.01701046 0.00077956
3-4:het:100Kb-1Mb  0.00815141 0.00000551 0.02323495 0.00188043 0.01200890084062 0.20570138 0.08651517
3-4:het:1Mb-10Mb   0.01439058 0.00003818 0.01723295 0.18503820 0.00000000000000 0.12230612 0.33498797
3-4:het:10Mb-40Mb  0.03273598 0.00189743 0.00618312 0.18827023 0.00227849015949 0.07593595 0.16201175
3-4:het:>40Mb      0.16670478 0.00450937 0.00048235 0.00053600 0.02652536185678 0.00256084 0.00119273
5-8:het:0-100Kb    0.00148480 0.00286475 0.01032126 0.00049621 0.00230818016157 0.00185133 0.01515300
5-8:het:100Kb-1Mb  0.00011311 0.00878768 0.04438502 0.01240360 0.02222437155571 0.02780896 0.14454268
5-8:het:1Mb-10Mb   0.00000032 0.00632529 0.08961901 0.12902796 0.14409609008673 0.02161426 0.10976846
                         CN21        CN22       CN23        CN24
0:homdel:0-100Kb   0.00000055 0.266866171 0.24410253 0.000371716
0:homdel:100Kb-1Mb 0.00022928 0.020384670 0.02413956 0.000760546
0:homdel:>1Mb      0.00135207 0.001282235 0.00355824 0.000575594
1:LOH:0-100Kb      0.00024820 0.021473560 0.13028998 0.000635022
1:LOH:100Kb-1Mb    0.01235880 0.034899515 0.07688590 0.004601138
1:LOH:1Mb-10Mb     0.05642821 0.024426895 0.03485188 0.004307654
1:LOH:10Mb-40Mb    0.04607252 0.003555775 0.02090447 0.002622552
1:LOH:>40Mb        0.01887089 0.002450425 0.00226301 0.002270070
2:LOH:0-100Kb      0.00070358 0.002994820 0.00000004 0.003253376
2:LOH:100Kb-1Mb    0.06234918 0.073916265 0.00033402 0.270457816
2:LOH:1Mb-10Mb     0.03913487 0.079960515 0.00178993 0.202204400
2:LOH:10Mb-40Mb    0.00129894 0.017654720 0.00517329 0.011946964
2:LOH:>40Mb        0.00195567 0.005905590 0.00000000 0.005078700
3-4:LOH:0-100Kb    0.00053506 0.001204125 0.00072698 0.000685112
3-4:LOH:100Kb-1Mb  0.00002091 0.008245880 0.00079858 0.011435602
3-4:LOH:1Mb-10Mb   0.00277049 0.010814625 0.00034028 0.005760546
3-4:LOH:10Mb-40Mb  0.00027444 0.003561930 0.00074860 0.000753150
3-4:LOH:>40Mb      0.00172068 0.005440365 0.00044828 0.000533794
5-8:LOH:0-100Kb    0.00000025 0.000741885 0.00000014 0.000227864
5-8:LOH:100Kb-1Mb  0.00005463 0.000521815 0.00000160 0.000577402
5-8:LOH:1Mb-10Mb   0.00001666 0.001434025 0.00001533 0.000810458
5-8:LOH:10Mb-40Mb  0.00000036 0.000605405 0.00000014 0.000114550
5-8:LOH:>40Mb      0.00003896 0.002408955 0.00001834 0.000086998
9+:LOH:0-100Kb     0.00000036 0.002498515 0.00000014 0.000492920
9+:LOH:100Kb-1Mb   0.00000397 0.000674480 0.00003275 0.000376804
9+:LOH:1Mb-10Mb    0.00008476 0.001078100 0.00000014 0.000121946
9+:LOH:10Mb-40Mb   0.00001589 0.000090180 0.00000014 0.000005706
9+:LOH:>40Mb       0.00005384 0.000104310 0.00000015 0.000002684
2:het:0-100Kb      0.00030646 0.003137450 0.00205934 0.000280432
2:het:100Kb-1Mb    0.01868806 0.030906700 0.02112224 0.020441704
2:het:1Mb-10Mb     0.12630566 0.161346311 0.12925873 0.196033892
2:het:10Mb-40Mb    0.20984674 0.108768015 0.26664244 0.179726574
2:het:>40Mb        0.07227018 0.000877650 0.01902544 0.018295890
3-4:het:0-100Kb    0.00800623 0.001840025 0.00074580 0.000505240
3-4:het:100Kb-1Mb  0.27819347 0.021454280 0.00157867 0.008474694
3-4:het:1Mb-10Mb   0.03014244 0.044882975 0.00634558 0.015763968
3-4:het:10Mb-40Mb  0.00614880 0.020714495 0.00077023 0.009131138
3-4:het:>40Mb      0.00000028 0.000519590 0.00000021 0.001866582
5-8:het:0-100Kb    0.00031093 0.000589460 0.00003532 0.002082402
5-8:het:100Kb-1Mb  0.00022234 0.001751590 0.00091931 0.004128916
5-8:het:1Mb-10Mb   0.00000972 0.004135055 0.00226165 0.005086422
 [ reached getOption("max.print") -- omitted 7 rows ]
> x2 = get_sig_db("CNS_TCGA")
> x2
$db
                              CN1            CN2        CN3        CN4         CN5          CN6
0:homdel:0-100Kb   0.001795053890 0.002237674329 0.06404424 0.00096628 0.025822490 0.0034924998
0:homdel:100Kb-1Mb 0.003807103951 0.007195787621 0.00640384 0.00021955 0.024993570 0.0075503095
0:homdel:>1Mb      0.002436746098 0.003837108012 0.01303343 0.00006124 0.003888700 0.0013361699
1:LOH:0-100Kb      0.002840449153 0.002826535986 0.06221358 0.05615077 0.015829115 0.0059558296
1:LOH:100Kb-1Mb    0.012263056631 0.006323914617 0.01261482 0.24779892 0.026544940 0.0105207593
1:LOH:1Mb-10Mb     0.019163417893 0.001023763998 0.01928346 0.08336934 0.001358030 0.0009915099
1:LOH:10Mb-40Mb    0.047297757322 0.000483364338 0.00871990 0.00010096 0.000573685 0.0004099400
1:LOH:>40Mb        0.073645998516 0.000124321668 0.00409212 0.00230378 0.000080995 0.0001791700
2:LOH:0-100Kb      0.001187984350 0.002488916646 0.00138849 0.01414630 0.013351500 0.0192514487
2:LOH:100Kb-1Mb    0.004303101724 0.019464869185 0.03383514 0.04008938 0.255496412 0.1772921576
2:LOH:1Mb-10Mb     0.004438012587 0.033551542805 0.01899058 0.00618009 0.264575824 0.1163828519
2:LOH:10Mb-40Mb    0.004318590464 0.052291174730 0.00267497 0.00024516 0.067065891 0.0063248096
2:LOH:>40Mb        0.012215653566 0.067374759875 0.00008237 0.00241502 0.019616490 0.0002609300
3-4:LOH:0-100Kb    0.001379947395 0.002717402002 0.00271910 0.01402566 0.005480255 0.0050518296
3-4:LOH:100Kb-1Mb  0.001667853035 0.013819445054 0.02381122 0.01144021 0.026855770 0.0135102791
3-4:LOH:1Mb-10Mb   0.001514284347 0.012471389014 0.03436767 0.00010785 0.029519046 0.0040970397
3-4:LOH:10Mb-40Mb  0.000102202610 0.010631238635 0.02189155 0.00000010 0.004552090 0.0000560700
3-4:LOH:>40Mb      0.007367609159 0.017426922018 0.02529479 0.00000013 0.000735890 0.0003285500
5-8:LOH:0-100Kb    0.000351297826 0.001689411337 0.00000053 0.02552717 0.000664530 0.0004894900
5-8:LOH:100Kb-1Mb  0.000212106955 0.003416253020 0.00256956 0.00169273 0.000652505 0.0003104600
5-8:LOH:1Mb-10Mb   0.000207783479 0.004495305663 0.00554920 0.00000019 0.000278185 0.0002143500
5-8:LOH:10Mb-40Mb  0.000099715217 0.002756042327 0.00000071 0.00001314 0.000125705 0.0001177100
5-8:LOH:>40Mb      0.000331938261 0.010089624349 0.00535955 0.00000014 0.000098750 0.0003040600
9+:LOH:0-100Kb     0.000133994783 0.000520196003 0.00000071 0.00001056 0.001312595 0.0049314197
9+:LOH:100Kb-1Mb   0.000411987828 0.000668643002 0.00216196 0.00000028 0.003306250 0.0054595396
9+:LOH:1Mb-10Mb    0.000200770001 0.000828997325 0.00220660 0.00000028 0.000649225 0.0008671599
9+:LOH:10Mb-40Mb   0.000006514783 0.000350903003 0.00211290 0.00000028 0.000015135 0.0000126800
9+:LOH:>40Mb       0.000002757826 0.000712768005 0.00092755 0.00000028 0.000012310 0.0000340000
2:het:0-100Kb      0.000126855217 0.001077283324 0.02085150 0.00018321 0.001733870 0.0035613998
2:het:100Kb-1Mb    0.002392692165 0.001448574994 0.01137198 0.00093060 0.008359660 0.0018074599
2:het:1Mb-10Mb     0.017226427425 0.000571467668 0.02363235 0.00124271 0.047988820 0.0086287494
2:het:10Mb-40Mb    0.112043886286 0.000401269997 0.02432782 0.00653021 0.040189910 0.0089315194
2:het:>40Mb        0.647548237436 0.000001616667 0.02278876 0.04721082 0.000000615 0.0020075299
3-4:het:0-100Kb    0.000986436966 0.001301612661 0.01675940 0.02839772 0.004295095 0.0094994693
3-4:het:100Kb-1Mb  0.003623146982 0.015217479637 0.04264799 0.20328865 0.027386325 0.2055037256
3-4:het:1Mb-10Mb   0.001734587400 0.058156429853 0.02762061 0.05567599 0.015401125 0.2333349037
3-4:het:10Mb-40Mb  0.003009542199 0.135200883071 0.01850544 0.00340995 0.020384580 0.0629906556
3-4:het:>40Mb      0.005373924797 0.390284779081 0.00000018 0.00472731 0.002974155 0.0024052698
5-8:het:0-100Kb    0.000741211739 0.001717200662 0.00551728 0.06860624 0.003368305 0.0036253197
5-8:het:100Kb-1Mb  0.000116379998 0.011630411571 0.03952374 0.05686576 0.007209015 0.0045492397
5-8:het:1Mb-10Mb   0.000204002174 0.019335547908 0.16260339 0.01134511 0.008309545 0.0020514199
5-8:het:10Mb-40Mb  0.000019348696 0.025641671295 0.12226601 0.00463152 0.000973130 0.0002642700
5-8:het:>40Mb      0.000525661739 0.044174807075 0.07693656 0.00000001 0.001276840 0.0000219000
9+:het:0-100Kb     0.000105258262 0.000991451008 0.00254618 0.00005163 0.003029025 0.0167008988
9+:het:100Kb-1Mb   0.000318177391 0.003241009627 0.00174383 0.00002151 0.007385620 0.0434289570
9+:het:1Mb-10Mb    0.000187035217 0.003779864641 0.00000071 0.00000026 0.006117540 0.0048971397
9+:het:10Mb-40Mb   0.000001743043 0.001908404344 0.00197462 0.00000024 0.000067940 0.0000335800
9+:het:>40Mb       0.000011755217 0.002099960351 0.00203108 0.00001474 0.000093000 0.0000235700
                          CN7         CN8            CN9       CN10       CN11       CN12        CN13
0:homdel:0-100Kb   0.00000000 0.000216260 0.008181841768 0.00779524 0.00161374 0.02309338 0.008542550
0:homdel:100Kb-1Mb 0.00000000 0.000720975 0.020999189073 0.03122532 0.00590270 0.05272477 0.018208835
0:homdel:>1Mb      0.00000000 0.000269340 0.009009219066 0.00455881 0.00313081 0.00686610 0.000509140
1:LOH:0-100Kb      0.00011082 0.000950405 0.018583651848 0.00879753 0.00275430 0.02182354 0.003672495
1:LOH:100Kb-1Mb    0.00504080 0.007283630 0.130807871527 0.03974523 0.00623170 0.06597701 0.014565860
1:LOH:1Mb-10Mb     0.00007442 0.002204905 0.159949199370 0.01091525 0.01775071 0.00423455 0.006219620
1:LOH:10Mb-40Mb    0.00000002 0.003664150 0.076229355119 0.00290428 0.00184154 0.00004033 0.001830770
1:LOH:>40Mb        0.00000000 0.006089315 0.027000692781 0.00148398 0.00005754 0.00000464 0.001703205
2:LOH:0-100Kb      0.00277607 0.011115840 0.004119057252 0.00635726 0.00148901 0.00590696 0.000472365
2:LOH:100Kb-1Mb    0.00454340 0.022282900 0.013774232673 0.08782354 0.01694496 0.08093648 0.013083940
2:LOH:1Mb-10Mb     0.00457336 0.008298320 0.011594392672 0.13191050 0.04392020 0.13267104 0.027714505
2:LOH:10Mb-40Mb    0.00004105 0.001159380 0.004945151804 0.08706983 0.02467614 0.17672789 0.061904045
2:LOH:>40Mb        0.00000000 0.000131970 0.002407304544 0.01593395 0.01121149 0.13622451 0.283071266
3-4:LOH:0-100Kb    0.00420447 0.009564720 0.001833529085 0.00743812 0.00158209 0.00930253 0.004443780
3-4:LOH:100Kb-1Mb  0.00232790 0.004662895 0.002848604541 0.06845530 0.04824190 0.03071852 0.021381520
3-4:LOH:1Mb-10Mb   0.00021573 0.003492150 0.003443509989 0.09646664 0.15626472 0.04005227 0.009517420
3-4:LOH:10Mb-40Mb  0.00000079 0.002194095 0.001390007273 0.04754809 0.05527416 0.02606018 0.001045855
3-4:LOH:>40Mb      0.00000674 0.003399115 0.001198600905 0.01319828 0.03509218 0.01659015 0.003249145
5-8:LOH:0-100Kb    0.00552275 0.010770475 0.000375937273 0.00260391 0.00501223 0.00578286 0.001066340
5-8:LOH:100Kb-1Mb  0.00682636 0.009675285 0.000836165454 0.02207809 0.04217432 0.00208666 0.000563220
5-8:LOH:1Mb-10Mb   0.00006776 0.002155840 0.000661617270 0.02022345 0.07357179 0.00322838 0.001505195
5-8:LOH:10Mb-40Mb  0.00000000 0.001022835 0.000376486361 0.00679665 0.01532663 0.00163617 0.000402270
5-8:LOH:>40Mb      0.00004933 0.001459620 0.000382634545 0.00017289 0.00347323 0.00110016 0.011616100
9+:LOH:0-100Kb     0.00632901 0.022043315 0.000759423640 0.00018531 0.00062013 0.00048688 0.000026095
9+:LOH:100Kb-1Mb   0.02139771 0.028381515 0.001234373638 0.00299660 0.01160088 0.00011188 0.000117410
9+:LOH:1Mb-10Mb    0.01464548 0.008094730 0.000574561822 0.00365022 0.02224864 0.00012019 0.000009970
9+:LOH:10Mb-40Mb   0.00000061 0.000025265 0.000010190000 0.00044558 0.00252885 0.00006139 0.000002465
9+:LOH:>40Mb       0.00000002 0.000111790 0.000004554545 0.00000009 0.00148788 0.00001647 0.000018935
2:het:0-100Kb      0.00021658 0.001038500 0.002813762724 0.00213926 0.00000000 0.00068448 0.002632120
2:het:100Kb-1Mb    0.00209292 0.000889200 0.057456734254 0.00460283 0.00000001 0.00313133 0.000689820
2:het:1Mb-10Mb     0.00016457 0.002329035 0.159920320844 0.00069290 0.00000000 0.00410482 0.000855655
2:het:10Mb-40Mb    0.00000000 0.002674940 0.129543643223 0.00078362 0.00000393 0.00107820 0.000937360
2:het:>40Mb        0.00000031 0.002161405 0.006767871088 0.00000006 0.00000008 0.00000043 0.004108450
3-4:het:0-100Kb    0.00362014 0.013551545 0.006686778158 0.00557084 0.00042229 0.00495000 0.001197990
3-4:het:100Kb-1Mb  0.06003456 0.041391180 0.067471317676 0.04177622 0.00000650 0.00936991 0.007901100
3-4:het:1Mb-10Mb   0.12143735 0.026193135 0.043510864271 0.08695636 0.01763335 0.01812126 0.057236571
3-4:het:10Mb-40Mb  0.00493032 0.004956070 0.007530375458 0.06757995 0.00761337 0.10067989 0.071385861
3-4:het:>40Mb      0.00022509 0.024168520 0.002876184608 0.00000001 0.00006203 0.00090365 0.352795454
5-8:het:0-100Kb    0.01467759 0.032617975 0.001719671803 0.00596208 0.00002945 0.00044794 0.000553290
5-8:het:100Kb-1Mb  0.16196039 0.127337371 0.001350210012 0.04005666 0.04380270 0.00783497 0.000657615
5-8:het:1Mb-10Mb   0.21136197 0.061241481 0.001136105468 0.01210908 0.18536884 0.00156351 0.000140470
5-8:het:10Mb-40Mb  0.00484320 0.008361195 0.000468091818 0.00183866 0.05728550 0.00131279 0.000333540
5-8:het:>40Mb      0.00032996 0.004528565 0.000413551812 0.00000000 0.01649539 0.00069671 0.002045620
9+:het:0-100Kb     0.02554054 0.094947456 0.001681830013 0.00047103 0.00000001 0.00002484 0.000001280
9+:het:100Kb-1Mb   0.16018674 0.266746762 0.004252060930 0.00025120 0.00000813 0.00018166 0.000000860
9+:het:1Mb-10Mb    0.14906452 0.110528846 0.000808817273 0.00000001 0.05279432 0.00016027 0.000000905
9+:het:10Mb-40Mb   0.00053612 0.001809925 0.000031166363 0.00012153 0.00605752 0.00013193 0.000020315
9+:het:>40Mb       0.00002253 0.001085855 0.000029286363 0.00030777 0.00039210 0.00003551 0.000041410
                         CN14       CN15             CN16       CN17       CN18       CN19
0:homdel:0-100Kb   0.00366730 0.00136668 0.00110894007763 0.00591472 0.00004078 0.00000055
0:homdel:100Kb-1Mb 0.00109281 0.00143123 0.00303045021213 0.00677398 0.00017845 0.00022928
0:homdel:>1Mb      0.04053983 0.00145330 0.00075840005309 0.00411050 0.00011722 0.00135207
1:LOH:0-100Kb      0.00142666 0.00211427 0.00155560010889 0.01041569 0.00050182 0.00024820
1:LOH:100Kb-1Mb    0.00580905 0.00507205 0.00141876009931 0.06429375 0.00081924 0.01235880
1:LOH:1Mb-10Mb     0.00343106 0.01868840 0.00028103001967 0.03777062 0.00624116 0.05642821
1:LOH:10Mb-40Mb    0.00204512 0.00550295 0.00000008000001 0.02105378 0.00283775 0.04607252
1:LOH:>40Mb        0.00064424 0.00000134 0.00000165000012 0.00174097 0.00001202 0.01887089
2:LOH:0-100Kb      0.00067984 0.00055893 0.00273632019154 0.00566334 0.00060974 0.00070358
2:LOH:100Kb-1Mb    0.01758306 0.00062269 0.00655180045863 0.05489644 0.00134094 0.06234918
2:LOH:1Mb-10Mb     0.01162738 0.08444233 0.00018517001296 0.11706714 0.01443458 0.03913487
2:LOH:10Mb-40Mb    0.00291477 0.08848328 0.00015695001099 0.04188772 0.00966270 0.00129894
2:LOH:>40Mb        0.00170498 0.00750380 0.00007257000508 0.03389879 0.00049936 0.00195567
3-4:LOH:0-100Kb    0.00093853 0.00267395 0.00226406015848 0.01388264 0.00256100 0.00053506
3-4:LOH:100Kb-1Mb  0.02159759 0.02375527 0.01402709098190 0.01258572 0.02182453 0.00002091
3-4:LOH:1Mb-10Mb   0.04370100 0.09462731 0.05963823417468 0.00110793 0.02055562 0.00277049
3-4:LOH:10Mb-40Mb  0.03291840 0.05183615 0.07185141502960 0.00278047 0.00224340 0.00027444
3-4:LOH:>40Mb      0.19071235 0.00224311 0.05059881354192 0.00421117 0.00094554 0.00172068
5-8:LOH:0-100Kb    0.00347840 0.00128554 0.00482129033749 0.00002587 0.00091844 0.00000025
5-8:LOH:100Kb-1Mb  0.00980644 0.00726579 0.02136849149579 0.00000814 0.00241053 0.00005463
5-8:LOH:1Mb-10Mb   0.01073875 0.01836005 0.04681185327683 0.00001578 0.00524955 0.00001666
5-8:LOH:10Mb-40Mb  0.00622641 0.00502947 0.02208834154618 0.00068876 0.00029923 0.00000036
5-8:LOH:>40Mb      0.01067078 0.00000129 0.00536994037590 0.00012041 0.00012116 0.00003896
9+:LOH:0-100Kb     0.00384194 0.00012468 0.00241473016903 0.00107168 0.00014531 0.00000036
9+:LOH:100Kb-1Mb   0.00471630 0.00005302 0.01211638084815 0.00117826 0.00085741 0.00000397
9+:LOH:1Mb-10Mb    0.00000235 0.00001369 0.01534961107447 0.00000016 0.00046208 0.00008476
9+:LOH:10Mb-40Mb   0.00000235 0.00005292 0.00097940006856 0.00000016 0.00010940 0.00001589
9+:LOH:>40Mb       0.00333085 0.00000029 0.00000077000005 0.00004662 0.00001071 0.00005384
2:het:0-100Kb      0.00266672 0.00038608 0.00029759002083 0.00311810 0.00053199 0.00030646
2:het:100Kb-1Mb    0.00197375 0.00018880 0.00003020000211 0.03122830 0.00464189 0.01868806
2:het:1Mb-10Mb     0.00185384 0.00087384 0.00000011000001 0.01642660 0.00278654 0.12630566
2:het:10Mb-40Mb    0.00136271 0.00061789 0.00000034000002 0.00452687 0.00139670 0.20984674
2:het:>40Mb        0.00000075 0.00000000 0.00000032000002 0.00000046 0.00000815 0.07227018
3-4:het:0-100Kb    0.00179605 0.00015917 0.00117086008196 0.01701046 0.00077956 0.00800623
3-4:het:100Kb-1Mb  0.02323495 0.00188043 0.01200890084062 0.20570138 0.08651517 0.27819347
3-4:het:1Mb-10Mb   0.01723295 0.18503820 0.00000000000000 0.12230612 0.33498797 0.03014244
3-4:het:10Mb-40Mb  0.00618312 0.18827023 0.00227849015949 0.07593595 0.16201175 0.00614880
3-4:het:>40Mb      0.00048235 0.00053600 0.02652536185678 0.00256084 0.00119273 0.00000028
5-8:het:0-100Kb    0.01032126 0.00049621 0.00230818016157 0.00185133 0.01515300 0.00031093
5-8:het:100Kb-1Mb  0.04438502 0.01240360 0.02222437155571 0.02780896 0.14454268 0.00022234
5-8:het:1Mb-10Mb   0.08961901 0.12902796 0.14409609008673 0.02161426 0.10976846 0.00000972
5-8:het:10Mb-40Mb  0.08336645 0.05516663 0.18136027269522 0.00344696 0.01800115 0.00012714
5-8:het:>40Mb      0.25307107 0.00000001 0.09531375667196 0.00000023 0.00182344 0.00247148
9+:het:0-100Kb     0.00338768 0.00005391 0.00934120065388 0.00503956 0.00357070 0.00005991
9+:het:100Kb-1Mb   0.00331660 0.00007486 0.05049958353497 0.00484797 0.00971177 0.00011614
9+:het:1Mb-10Mb    0.00998959 0.00013899 0.08409049588633 0.01332158 0.00568101 0.00000036
9+:het:10Mb-40Mb   0.00316669 0.00012341 0.01848061129364 0.00001563 0.00085042 0.00015659
9+:het:>40Mb       0.00674090 0.00000001 0.00241512016906 0.00002722 0.00003526 0.00002306

$aetiology
                                          aetiology
CN1  See https://cancer.sanger.ac.uk/signatures/cn/
CN2  See https://cancer.sanger.ac.uk/signatures/cn/
CN3  See https://cancer.sanger.ac.uk/signatures/cn/
CN4  See https://cancer.sanger.ac.uk/signatures/cn/
CN5  See https://cancer.sanger.ac.uk/signatures/cn/
CN6  See https://cancer.sanger.ac.uk/signatures/cn/
CN7  See https://cancer.sanger.ac.uk/signatures/cn/
CN8  See https://cancer.sanger.ac.uk/signatures/cn/
CN9  See https://cancer.sanger.ac.uk/signatures/cn/
CN10 See https://cancer.sanger.ac.uk/signatures/cn/
CN11 See https://cancer.sanger.ac.uk/signatures/cn/
CN12 See https://cancer.sanger.ac.uk/signatures/cn/
CN13 See https://cancer.sanger.ac.uk/signatures/cn/
CN14 See https://cancer.sanger.ac.uk/signatures/cn/
CN15 See https://cancer.sanger.ac.uk/signatures/cn/
CN16 See https://cancer.sanger.ac.uk/signatures/cn/
CN17 See https://cancer.sanger.ac.uk/signatures/cn/
CN18 See https://cancer.sanger.ac.uk/signatures/cn/
CN19 See https://cancer.sanger.ac.uk/signatures/cn/

$date
[1] "2021/07/23"

> rownames(x$db) == rownames(x2$db)
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[20] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[39] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> all(rownames(x$db) == rownames(x2$db))
[1] TRUE