R/discovery_prediction.R
predict_exposure.RdExposures for samples will be predicted using an existing set
of signatures stored in a musica_result object.
Algorithms available for prediction include a modify version of "lda",
"decompTumor2Sig", and "deconstructSigs".
predict_exposure( musica, g, table_name, signature_res, algorithm = c("lda", "decompTumor2Sig", "deconstructSigs"), signatures_to_use = seq_len(ncol(signatures(signature_res))), verbose = FALSE )
| musica | A |
|---|---|
| g | A BSgenome object indicating which genome
reference the variants and their coordinates were derived from. Only used
if |
| table_name | Name of table used for posterior prediction. Must match the table type used to generate the prediction signatures |
| signature_res | Signatures used to predict exposures for the samples
|
| algorithm | Algorithm to use for prediction of exposures. One of
|
| signatures_to_use | Which signatures in the |
| verbose | If |
Returns a A musica_result object containing
signatures given by the signature_res parameter and exposures
predicted from these signatures.
data(musica) data(cosmic_v2_sigs) g <- select_genome("19") build_standard_table(musica, g, "SBS96", overwrite = TRUE) #> Building count table from SBS with SBS96 schema #> Warning: Overwriting counts table: SBS96 result <- predict_exposure(musica = musica, table_name = "SBS96", signature_res = cosmic_v2_sigs, algorithm = "lda") # Predict using LDA-like algorithm with seed set to 1 set.seed(1) predict_exposure(musica = musica, table_name = "SBS96", signature_res = cosmic_v2_sigs, algorithm = "lda") #> An object of class "musica_result" #> Slot "signatures": #> Signature1 Signature2 Signature3 Signature4 Signature5 #> C>A_ACA 1.109833e-02 6.827082e-04 0.0221723068 0.0365 0.0149415477 #> C>A_ACC 9.149341e-03 6.191072e-04 0.0178716754 0.0309 0.0089609180 #> C>A_ACG 1.490070e-03 9.927896e-05 0.0021383396 0.0183 0.0022078460 #> C>A_ACT 6.233885e-03 3.238914e-04 0.0162651456 0.0243 0.0092069053 #> C>A_CCA 6.595870e-03 6.774450e-04 0.0187817256 0.0461 0.0096749043 #> C>A_CCC 7.342368e-03 2.136810e-04 0.0157604578 0.0614 0.0049523006 #> C>A_CCG 8.928404e-04 6.770460e-06 0.0019633898 0.0088 0.0028006273 #> C>A_CCT 7.186582e-03 4.163329e-04 0.0147228611 0.0432 0.0110134658 #> C>A_GCA 8.232604e-03 3.520134e-04 0.0096965397 0.0376 0.0118921690 #> C>A_GCC 5.758021e-03 1.338169e-04 0.0108433411 0.0399 0.0092478575 #> C>A_GCG 6.163352e-04 1.784417e-04 0.0009291405 0.0227 0.0028091885 #> C>A_GCT 4.459080e-03 1.228320e-04 0.0122153826 0.0258 0.0103012675 #> C>A_TCA 1.225006e-02 1.512743e-02 0.0116532249 0.0330 0.0147740162 #> C>A_TCC 1.116223e-02 6.532492e-03 0.0166067750 0.0538 0.0120434650 #> C>A_TCG 2.275496e-03 1.656455e-03 0.0013572394 0.0104 0.0039023624 #> C>A_TCT 1.525910e-02 1.239461e-02 0.0163280760 0.0370 0.0182433957 #> C>G_ACA 1.801068e-03 2.634810e-04 0.0240026152 0.0097 0.0116710217 #> C>G_ACC 2.580909e-03 2.698660e-04 0.0121603037 0.0054 0.0072920886 #> C>G_ACG 5.925480e-04 2.192339e-04 0.0052754195 0.0031 0.0023038392 #> C>G_ACT 2.963986e-03 6.109735e-04 0.0232776563 0.0054 0.0116962457 #> C>G_CCA 1.284983e-03 2.777208e-05 0.0168325720 0.0105 0.0075375232 #> C>G_CCC 7.021348e-04 2.796439e-04 0.0135314415 0.0097 0.0076332267 #> C>G_CCG 5.062896e-04 1.916158e-05 0.0041764575 0.0063 0.0026137604 #> C>G_CCT 1.381543e-03 3.127816e-04 0.0240463904 0.0094 0.0094170979 #> C>G_GCA 6.021227e-04 4.483851e-05 0.0119168446 0.0070 0.0055594231 #> C>G_GCC 2.393352e-03 1.452010e-05 0.0098236534 0.0091 0.0053888012 #> C>G_GCG 2.485340e-07 4.066589e-05 0.0016710543 0.0062 0.0011005896 #> C>G_GCT 8.900807e-04 2.684295e-04 0.0179143343 0.0060 0.0060412478 #> C>G_TCA 1.874853e-03 3.724185e-02 0.0160414054 0.0032 0.0026810570 #> C>G_TCC 2.067419e-03 1.941341e-05 0.0201499204 0.0105 0.0079240483 #> C>G_TCG 3.048970e-04 1.625465e-03 0.0025279109 0.0031 0.0013190756 #> C>G_TCT 3.151574e-03 6.687990e-02 0.0326736408 0.0050 0.0066445957 #> C>T_ACA 2.951453e-02 7.441557e-03 0.0178721707 0.0120 0.0218391876 #> C>T_ACC 1.432275e-02 2.726312e-03 0.0088960343 0.0075 0.0127561056 #> C>T_ACG 1.716469e-01 3.322083e-03 0.0035727083 0.0028 0.0167601771 #> C>T_ACT 1.262376e-02 3.326528e-03 0.0147976122 0.0059 0.0164779547 #> C>T_CCA 2.089645e-02 1.501951e-02 0.0143950595 0.0210 0.0227692094 #> C>T_CCC 1.850170e-02 3.516918e-03 0.0085447812 0.0144 0.0175094763 #> C>T_CCG 9.557722e-02 4.979276e-03 0.0035184658 0.0076 0.0128622376 #> C>T_CCT 1.711331e-02 8.956553e-03 0.0160755457 0.0201 0.0204295134 #> C>T_GCA 2.494381e-02 6.390808e-03 0.0161272733 0.0087 0.0200382586 #> C>T_GCC 2.716149e-02 1.995817e-03 0.0082086324 0.0080 0.0180223122 #> C>T_GCG 1.035708e-01 3.030210e-04 0.0012129229 0.0023 0.0131938176 #> C>T_GCT 1.768985e-02 3.265818e-03 0.0106116492 0.0082 0.0195029153 #> C>T_TCA 1.449210e-02 4.199414e-01 0.0088802091 0.0035 0.0109975603 #> C>T_TCC 1.768078e-02 8.197250e-02 0.0135295728 0.0070 0.0206449648 #> C>T_TCG 7.600222e-02 4.772019e-02 0.0017054089 0.0011 0.0075344896 #> C>T_TCT 1.376170e-02 2.286749e-01 0.0103044169 0.0077 0.0117874618 #> T>A_ATA 4.021520e-03 1.323770e-07 0.0084285636 0.0048 0.0089029043 #> T>A_ATC 2.371144e-03 1.130696e-04 0.0073730967 0.0039 0.0073992025 #> T>A_ATG 2.810910e-03 5.329294e-04 0.0073573000 0.0100 0.0115080515 #> T>A_ATT 8.360909e-03 1.491110e-04 0.0087539390 0.0030 0.0111936232 #> T>A_CTA 1.182587e-03 1.545990e-04 0.0075713203 0.0075 0.0050431635 #> T>A_CTC 1.903167e-03 4.640190e-04 0.0127254635 0.0111 0.0062088437 #> T>A_CTG 1.487961e-03 2.304098e-04 0.0115085619 0.0342 0.0105075690 #> T>A_CTT 2.179344e-03 5.748856e-04 0.0164561777 0.0115 0.0097846407 #> T>A_GTA 6.892894e-04 1.149942e-04 0.0044347826 0.0069 0.0067403877 #> T>A_GTC 5.524095e-04 2.938621e-04 0.0056154324 0.0052 0.0040215965 #> T>A_GTG 1.200229e-03 8.872134e-05 0.0080701365 0.0133 0.0068143523 #> T>A_GTT 2.107137e-03 2.157555e-04 0.0086791217 0.0045 0.0051010329 #> T>A_TTA 5.600155e-03 8.075249e-05 0.0071326814 0.0045 0.0092056373 #> T>A_TTC 1.999079e-03 4.802898e-06 0.0091027978 0.0046 0.0068353442 #> T>A_TTG 1.090066e-03 6.660504e-05 0.0065658630 0.0082 0.0071442088 #> T>A_TTT 3.981023e-03 2.763159e-04 0.0147121354 0.0045 0.0102408504 #> T>C_ATA 1.391577e-02 1.303510e-03 0.0130357094 0.0084 0.0353667351 #> T>C_ATC 6.274961e-03 4.255767e-04 0.0091862897 0.0020 0.0137711021 #> T>C_ATG 1.013764e-02 5.754730e-04 0.0117169201 0.0081 0.0284490517 #> T>C_ATT 9.256316e-03 1.488164e-03 0.0169788708 0.0036 0.0273029742 #> T>C_CTA 4.176675e-03 5.466192e-04 0.0078950126 0.0052 0.0142386298 #> T>C_CTC 5.252593e-03 3.923326e-04 0.0144311704 0.0026 0.0124895004 #> T>C_CTG 7.013225e-03 3.620245e-04 0.0084229721 0.0100 0.0187416312 #> T>C_CTT 6.713813e-03 5.609001e-04 0.0119324305 0.0054 0.0190540829 #> T>C_GTA 1.124784e-02 4.673852e-06 0.0068500556 0.0061 0.0162949828 #> T>C_GTC 6.999724e-03 1.860659e-04 0.0062607490 0.0016 0.0095745606 #> T>C_GTG 4.977593e-03 4.950440e-07 0.0060987630 0.0042 0.0141039293 #> T>C_GTT 1.066741e-02 5.785981e-04 0.0075093439 0.0024 0.0156668747 #> T>C_TTA 8.073616e-03 1.019324e-04 0.0091154951 0.0028 0.0170596410 #> T>C_TTC 4.857381e-03 4.703437e-04 0.0109537909 0.0016 0.0141957091 #> T>C_TTG 8.325454e-03 1.923542e-04 0.0061130332 0.0036 0.0125965017 #> T>C_TTT 6.257106e-03 5.853303e-04 0.0107743363 0.0022 0.0173751391 #> T>G_ATA 1.587636e-03 3.371841e-05 0.0023513681 0.0000 0.0034621520 #> T>G_ATC 1.784091e-03 2.484483e-05 0.0014642311 0.0002 0.0022465927 #> T>G_ATG 1.385831e-03 2.734541e-04 0.0090537776 0.0015 0.0054902168 #> T>G_ATT 3.158539e-03 2.176949e-04 0.0070309764 0.0002 0.0038212267 #> T>G_CTA 3.026912e-04 1.137846e-04 0.0019741811 0.0000 0.0020416489 #> T>G_CTC 2.098502e-03 2.209509e-05 0.0058242955 0.0013 0.0034785021 #> T>G_CTG 1.599549e-03 2.282459e-04 0.0104646545 0.0046 0.0071474562 #> T>G_CTT 2.758538e-03 6.711134e-05 0.0087243873 0.0012 0.0114868115 #> T>G_GTA 9.904500e-05 9.555239e-05 0.0041444880 0.0000 0.0016276645 #> T>G_GTC 2.023656e-04 4.700238e-05 0.0045019853 0.0000 0.0003277349 #> T>G_GTG 1.188353e-03 1.099257e-04 0.0163914526 0.0018 0.0059488798 #> T>G_GTT 8.007233e-04 8.647718e-05 0.0070672366 0.0002 0.0033074666 #> T>G_TTA 1.397554e-03 7.173695e-05 0.0054271842 0.0000 0.0052028744 #> T>G_TTC 1.291737e-03 1.428146e-05 0.0061602504 0.0003 0.0051316079 #> T>G_TTG 2.031077e-03 2.066152e-04 0.0110765263 0.0030 0.0060552541 #> T>G_TTT 4.030128e-03 2.359820e-05 0.0130009842 0.0011 0.0133699358 #> Signature6 Signature7 Signature8 Signature9 Signature10 Signature11 #> C>A_ACA 0.0017 0.0004 3.671800e-02 0.0120 0.0007 0.0002 #> C>A_ACC 0.0028 0.0005 3.324572e-02 0.0067 0.0010 0.0010 #> C>A_ACG 0.0005 0.0000 2.525311e-03 0.0005 0.0003 0.0000 #> C>A_ACT 0.0019 0.0004 3.359855e-02 0.0068 0.0092 0.0002 #> C>A_CCA 0.0101 0.0012 3.172376e-02 0.0098 0.0031 0.0007 #> C>A_CCC 0.0241 0.0006 2.550541e-02 0.0057 0.0009 0.0017 #> C>A_CCG 0.0091 0.0000 1.159624e-03 0.0000 0.0007 0.0010 #> C>A_CCT 0.0571 0.0013 2.879117e-02 0.0091 0.0160 0.0014 #> C>A_GCA 0.0024 0.0003 2.368233e-02 0.0118 0.0014 0.0004 #> C>A_GCC 0.0058 0.0001 1.582190e-02 0.0092 0.0022 0.0010 #> C>A_GCG 0.0021 0.0000 8.509138e-04 0.0000 0.0002 0.0000 #> C>A_GCT 0.0087 0.0001 2.106124e-02 0.0085 0.0088 0.0006 #> C>A_TCA 0.0017 0.0010 2.703238e-02 0.0222 0.0374 0.0009 #> C>A_TCC 0.0029 0.0020 1.808977e-02 0.0043 0.0103 0.0025 #> C>A_TCG 0.0011 0.0002 1.694875e-03 0.0000 0.0031 0.0001 #> C>A_TCT 0.0058 0.0013 3.814133e-02 0.0322 0.3083 0.0004 #> C>G_ACA 0.0013 0.0000 8.356845e-03 0.0048 0.0005 0.0007 #> C>G_ACC 0.0012 0.0000 4.306380e-03 0.0023 0.0003 0.0003 #> C>G_ACG 0.0000 0.0000 5.844153e-04 0.0000 0.0000 0.0000 #> C>G_ACT 0.0018 0.0001 8.634907e-03 0.0038 0.0002 0.0009 #> C>G_CCA 0.0000 0.0001 6.619077e-03 0.0018 0.0000 0.0000 #> C>G_CCC 0.0000 0.0004 6.077703e-03 0.0020 0.0000 0.0002 #> C>G_CCG 0.0000 0.0006 6.560334e-04 0.0000 0.0000 0.0008 #> C>G_CCT 0.0002 0.0003 7.805027e-03 0.0039 0.0000 0.0002 #> C>G_GCA 0.0000 0.0000 3.724568e-03 0.0011 0.0000 0.0000 #> C>G_GCC 0.0030 0.0004 3.046597e-03 0.0029 0.0002 0.0002 #> C>G_GCG 0.0000 0.0000 3.212128e-04 0.0000 0.0000 0.0000 #> C>G_GCT 0.0017 0.0000 5.775664e-03 0.0044 0.0004 0.0000 #> C>G_TCA 0.0000 0.0002 4.117879e-03 0.0033 0.0000 0.0001 #> C>G_TCC 0.0002 0.0010 3.799650e-03 0.0025 0.0000 0.0011 #> C>G_TCG 0.0000 0.0003 2.565302e-05 0.0000 0.0000 0.0003 #> C>G_TCT 0.0001 0.0007 6.247554e-03 0.0049 0.0001 0.0008 #> C>T_ACA 0.0312 0.0000 1.806669e-02 0.0093 0.0000 0.0225 #> C>T_ACC 0.0163 0.0197 5.650015e-03 0.0056 0.0032 0.1099 #> C>T_ACG 0.0908 0.0001 1.926511e-02 0.0125 0.0126 0.0072 #> C>T_ACT 0.0149 0.0043 2.080597e-02 0.0076 0.0047 0.0639 #> C>T_CCA 0.0085 0.0754 4.865810e-03 0.0098 0.0012 0.0310 #> C>T_CCC 0.0099 0.1007 3.980150e-03 0.0069 0.0024 0.1518 #> C>T_CCG 0.0901 0.0208 8.338639e-03 0.0076 0.0109 0.0135 #> C>T_CCT 0.0087 0.0788 1.884363e-02 0.0097 0.0043 0.0816 #> C>T_GCA 0.0653 0.0000 2.261263e-03 0.0062 0.0000 0.0261 #> C>T_GCC 0.0773 0.0210 1.616649e-03 0.0069 0.0134 0.0975 #> C>T_GCG 0.1339 0.0002 1.160671e-02 0.0088 0.0270 0.0090 #> C>T_GCT 0.0524 0.0161 6.284929e-03 0.0101 0.0152 0.0522 #> C>T_TCA 0.0074 0.1202 7.180669e-03 0.0050 0.0037 0.0302 #> C>T_TCC 0.0067 0.2887 4.061033e-03 0.0084 0.0211 0.1589 #> C>T_TCG 0.0391 0.0992 5.535122e-03 0.0047 0.2141 0.0080 #> C>T_TCT 0.0047 0.0844 1.220907e-02 0.0096 0.0392 0.0954 #> T>A_ATA 0.0006 0.0010 1.336508e-02 0.0121 0.0000 0.0002 #> T>A_ATC 0.0033 0.0008 1.243120e-02 0.0042 0.0002 0.0001 #> T>A_ATG 0.0000 0.0009 1.403666e-02 0.0068 0.0000 0.0007 #> T>A_ATT 0.0053 0.0035 2.410992e-02 0.0185 0.0012 0.0003 #> T>A_CTA 0.0001 0.0000 1.202422e-02 0.0055 0.0000 0.0004 #> T>A_CTC 0.0026 0.0014 1.788109e-02 0.0049 0.0001 0.0011 #> T>A_CTG 0.0008 0.0007 1.635677e-02 0.0051 0.0003 0.0006 #> T>A_CTT 0.0011 0.0018 2.624780e-02 0.0069 0.0009 0.0004 #> T>A_GTA 0.0000 0.0000 8.139179e-03 0.0030 0.0000 0.0003 #> T>A_GTC 0.0028 0.0000 7.910080e-03 0.0029 0.0001 0.0003 #> T>A_GTG 0.0006 0.0006 9.057263e-03 0.0028 0.0000 0.0004 #> T>A_GTT 0.0021 0.0010 1.781224e-02 0.0036 0.0004 0.0001 #> T>A_TTA 0.0002 0.0010 1.514000e-02 0.0215 0.0000 0.0003 #> T>A_TTC 0.0008 0.0015 1.209355e-02 0.0027 0.0008 0.0000 #> T>A_TTG 0.0000 0.0010 8.362547e-03 0.0140 0.0000 0.0000 #> T>A_TTT 0.0007 0.0050 2.765330e-02 0.0139 0.0028 0.0008 #> T>C_ATA 0.0075 0.0005 1.620651e-02 0.0252 0.0031 0.0006 #> T>C_ATC 0.0056 0.0001 7.787803e-03 0.0105 0.0052 0.0015 #> T>C_ATG 0.0217 0.0007 9.852584e-03 0.0176 0.0026 0.0008 #> T>C_ATT 0.0023 0.0011 2.182946e-02 0.0247 0.0040 0.0003 #> T>C_CTA 0.0062 0.0010 5.173842e-03 0.0154 0.0005 0.0001 #> T>C_CTC 0.0040 0.0008 1.093689e-02 0.0118 0.0019 0.0004 #> T>C_CTG 0.0270 0.0010 5.657774e-03 0.0154 0.0015 0.0001 #> T>C_CTT 0.0033 0.0045 1.112039e-02 0.0275 0.0020 0.0009 #> T>C_GTA 0.0122 0.0002 5.720779e-03 0.0091 0.0064 0.0010 #> T>C_GTC 0.0059 0.0001 5.181052e-03 0.0097 0.0101 0.0016 #> T>C_GTG 0.0115 0.0003 5.040707e-03 0.0094 0.0054 0.0019 #> T>C_GTT 0.0042 0.0081 8.488220e-03 0.0126 0.0124 0.0023 #> T>C_TTA 0.0059 0.0023 4.901072e-03 0.0156 0.0030 0.0002 #> T>C_TTC 0.0035 0.0018 6.081011e-03 0.0137 0.0097 0.0009 #> T>C_TTG 0.0106 0.0019 1.712485e-03 0.0098 0.0065 0.0007 #> T>C_TTT 0.0029 0.0024 1.000344e-02 0.0309 0.0099 0.0005 #> T>G_ATA 0.0000 0.0000 4.219719e-03 0.0335 0.0000 0.0000 #> T>G_ATC 0.0017 0.0000 7.936713e-04 0.0051 0.0040 0.0000 #> T>G_ATG 0.0007 0.0009 6.865800e-03 0.0052 0.0015 0.0001 #> T>G_ATT 0.0029 0.0000 2.939922e-03 0.0193 0.0137 0.0000 #> T>G_CTA 0.0001 0.0000 2.424051e-03 0.0216 0.0022 0.0000 #> T>G_CTC 0.0040 0.0008 2.096211e-03 0.0064 0.0018 0.0001 #> T>G_CTG 0.0050 0.0009 6.604046e-03 0.0126 0.0037 0.0011 #> T>G_CTT 0.0086 0.0013 4.866714e-03 0.0509 0.0182 0.0009 #> T>G_GTA 0.0000 0.0000 9.745787e-04 0.0072 0.0000 0.0000 #> T>G_GTC 0.0016 0.0000 5.248216e-04 0.0006 0.0020 0.0000 #> T>G_GTG 0.0010 0.0017 6.087753e-03 0.0050 0.0009 0.0010 #> T>G_GTT 0.0035 0.0009 5.427434e-03 0.0185 0.0030 0.0000 #> T>G_TTA 0.0009 0.0000 1.743221e-03 0.0502 0.0050 0.0000 #> T>G_TTC 0.0019 0.0010 2.549838e-03 0.0081 0.0092 0.0000 #> T>G_TTG 0.0011 0.0010 6.030395e-03 0.0088 0.0022 0.0003 #> T>G_TTT 0.0072 0.0014 7.223999e-03 0.0545 0.0633 0.0003 #> Signature12 Signature13 Signature14 Signature15 Signature16 #> C>A_ACA 0.0077 3.347572e-04 0.0001 0.0013 0.0161 #> C>A_ACC 0.0047 6.487361e-04 0.0042 0.0040 0.0097 #> C>A_ACG 0.0017 3.814459e-05 0.0005 0.0000 0.0022 #> C>A_ACT 0.0046 8.466585e-04 0.0296 0.0057 0.0088 #> C>A_CCA 0.0135 1.710090e-03 0.0056 0.0106 0.0159 #> C>A_CCC 0.0112 1.159257e-03 0.0102 0.0084 0.0100 #> C>A_CCG 0.0028 2.441665e-04 0.0009 0.0015 0.0022 #> C>A_CCT 0.0071 1.256768e-03 0.1257 0.0228 0.0084 #> C>A_GCA 0.0062 1.321096e-04 0.0018 0.0024 0.0096 #> C>A_GCC 0.0056 7.542440e-04 0.0114 0.0099 0.0094 #> C>A_GCG 0.0015 9.682078e-05 0.0011 0.0013 0.0036 #> C>A_GCT 0.0027 5.511037e-04 0.0736 0.0309 0.0063 #> C>A_TCA 0.0066 4.816605e-02 0.0005 0.0057 0.0122 #> C>A_TCC 0.0099 1.732956e-02 0.0166 0.0062 0.0145 #> C>A_TCG 0.0019 2.293157e-03 0.0000 0.0025 0.0040 #> C>A_TCT 0.0049 1.863458e-02 0.0516 0.0145 0.0157 #> C>G_ACA 0.0031 3.775165e-03 0.0001 0.0011 0.0048 #> C>G_ACC 0.0015 9.208248e-04 0.0000 0.0001 0.0024 #> C>G_ACG 0.0000 1.989049e-05 0.0000 0.0006 0.0000 #> C>G_ACT 0.0025 3.860632e-03 0.0001 0.0010 0.0073 #> C>G_CCA 0.0019 5.333651e-03 0.0000 0.0009 0.0040 #> C>G_CCC 0.0019 9.123035e-04 0.0000 0.0003 0.0050 #> C>G_CCG 0.0000 2.854673e-04 0.0000 0.0004 0.0028 #> C>G_CCT 0.0019 6.383098e-03 0.0000 0.0017 0.0080 #> C>G_GCA 0.0012 1.349420e-03 0.0002 0.0022 0.0031 #> C>G_GCC 0.0011 7.888077e-04 0.0001 0.0005 0.0032 #> C>G_GCG 0.0000 8.179121e-05 0.0000 0.0006 0.0000 #> C>G_GCT 0.0009 2.680123e-03 0.0003 0.0018 0.0029 #> C>G_TCA 0.0024 2.802349e-01 0.0000 0.0009 0.0050 #> C>G_TCC 0.0027 6.388529e-02 0.0000 0.0026 0.0064 #> C>G_TCG 0.0000 9.528486e-03 0.0000 0.0000 0.0000 #> C>G_TCT 0.0015 3.302255e-01 0.0001 0.0015 0.0169 #> C>T_ACA 0.0121 1.480181e-03 0.0293 0.0117 0.0135 #> C>T_ACC 0.0054 4.050871e-05 0.0321 0.0169 0.0076 #> C>T_ACG 0.0019 3.165947e-04 0.0496 0.0309 0.0035 #> C>T_ACT 0.0067 0.000000e+00 0.0277 0.0066 0.0101 #> C>T_CCA 0.0187 3.647278e-03 0.0060 0.0051 0.0210 #> C>T_CCC 0.0094 1.004229e-03 0.0167 0.0088 0.0098 #> C>T_CCG 0.0046 1.292021e-04 0.0293 0.0155 0.0016 #> C>T_CCT 0.0205 6.117700e-04 0.0186 0.0096 0.0211 #> C>T_GCA 0.0124 2.934138e-03 0.0557 0.0476 0.0125 #> C>T_GCC 0.0092 2.515171e-03 0.0618 0.1345 0.0092 #> C>T_GCG 0.0023 3.205265e-03 0.0978 0.1829 0.0009 #> C>T_GCT 0.0115 1.687731e-03 0.0555 0.0800 0.0116 #> C>T_TCA 0.0138 1.138421e-01 0.0092 0.0112 0.0172 #> C>T_TCC 0.0095 1.502484e-02 0.0283 0.0156 0.0131 #> C>T_TCG 0.0010 6.102098e-03 0.0094 0.0104 0.0036 #> C>T_TCT 0.0090 2.814066e-02 0.0229 0.0076 0.0193 #> T>A_ATA 0.0058 1.243618e-03 0.0000 0.0021 0.0081 #> T>A_ATC 0.0065 1.060002e-03 0.0008 0.0090 0.0073 #> T>A_ATG 0.0046 1.025544e-04 0.0000 0.0009 0.0080 #> T>A_ATT 0.0060 9.718121e-04 0.0009 0.0079 0.0084 #> T>A_CTA 0.0017 2.851590e-04 0.0000 0.0016 0.0054 #> T>A_CTC 0.0086 2.222873e-04 0.0034 0.0043 0.0128 #> T>A_CTG 0.0031 2.869518e-04 0.0002 0.0027 0.0130 #> T>A_CTT 0.0054 8.004460e-07 0.0020 0.0007 0.0096 #> T>A_GTA 0.0015 1.379604e-04 0.0000 0.0000 0.0030 #> T>A_GTC 0.0039 2.528674e-04 0.0025 0.0038 0.0040 #> T>A_GTG 0.0019 1.535175e-04 0.0000 0.0026 0.0051 #> T>A_GTT 0.0031 1.227456e-04 0.0009 0.0043 0.0033 #> T>A_TTA 0.0057 4.032613e-04 0.0000 0.0008 0.0085 #> T>A_TTC 0.0132 7.718133e-04 0.0016 0.0019 0.0087 #> T>A_TTG 0.0037 2.451942e-04 0.0000 0.0006 0.0063 #> T>A_TTT 0.0094 1.603460e-04 0.0012 0.0003 0.0080 #> T>C_ATA 0.0466 5.494542e-04 0.0026 0.0115 0.0717 #> T>C_ATC 0.0317 1.455067e-04 0.0046 0.0073 0.0171 #> T>C_ATG 0.0487 2.791780e-04 0.0035 0.0073 0.0348 #> T>C_ATT 0.0250 2.674614e-04 0.0025 0.0063 0.0497 #> T>C_CTA 0.0312 4.275147e-05 0.0006 0.0032 0.0146 #> T>C_CTC 0.0385 4.330754e-05 0.0053 0.0050 0.0194 #> T>C_CTG 0.0415 5.427253e-05 0.0016 0.0128 0.0190 #> T>C_CTT 0.0324 7.639440e-07 0.0027 0.0035 0.0263 #> T>C_GTA 0.0573 1.054081e-03 0.0078 0.0195 0.0161 #> T>C_GTC 0.0274 5.298997e-04 0.0127 0.0499 0.0099 #> T>C_GTG 0.0410 6.300957e-04 0.0082 0.0154 0.0148 #> T>C_GTT 0.0405 6.761879e-04 0.0086 0.0094 0.0142 #> T>C_TTA 0.0500 7.840561e-04 0.0018 0.0068 0.0246 #> T>C_TTC 0.0342 1.329749e-04 0.0056 0.0099 0.0183 #> T>C_TTG 0.0320 3.740240e-05 0.0034 0.0039 0.0165 #> T>C_TTT 0.0371 1.797028e-04 0.0026 0.0047 0.0174 #> T>G_ATA 0.0012 3.861998e-04 0.0000 0.0000 0.0052 #> T>G_ATC 0.0010 1.123832e-04 0.0020 0.0006 0.0042 #> T>G_ATG 0.0018 3.600070e-05 0.0007 0.0012 0.0061 #> T>G_ATT 0.0030 1.924938e-04 0.0056 0.0029 0.0076 #> T>G_CTA 0.0013 1.509421e-05 0.0000 0.0000 0.0002 #> T>G_CTC 0.0049 1.476248e-04 0.0020 0.0019 0.0082 #> T>G_CTG 0.0045 4.598730e-05 0.0005 0.0007 0.0067 #> T>G_CTT 0.0063 4.637147e-04 0.0063 0.0045 0.0186 #> T>G_GTA 0.0000 1.848986e-05 0.0000 0.0000 0.0000 #> T>G_GTC 0.0004 9.337351e-05 0.0019 0.0022 0.0032 #> T>G_GTG 0.0011 1.057919e-05 0.0012 0.0037 0.0008 #> T>G_GTT 0.0032 5.374121e-05 0.0038 0.0190 0.0044 #> T>G_TTA 0.0019 5.465818e-04 0.0000 0.0000 0.0068 #> T>G_TTC 0.0027 2.353471e-04 0.0015 0.0004 0.0069 #> T>G_TTG 0.0011 4.790220e-07 0.0002 0.0009 0.0049 #> T>G_TTT 0.0032 6.705883e-04 0.0025 0.0033 0.0163 #> Signature17 Signature18 Signature19 Signature20 Signature21 #> C>A_ACA 1.832019e-03 5.053642e-02 0.0107 1.179962e-03 0.0001 #> C>A_ACC 3.422356e-04 1.093982e-02 0.0074 2.211505e-03 0.0007 #> C>A_ACG 1.576225e-06 2.288073e-03 0.0005 1.616910e-07 0.0000 #> C>A_ACT 3.179665e-03 1.942409e-02 0.0074 3.008010e-03 0.0006 #> C>A_CCA 1.032430e-03 8.876811e-02 0.0112 1.737711e-02 0.0020 #> C>A_CCC 4.218801e-04 2.064139e-02 0.0159 3.650246e-02 0.0014 #> C>A_CCG 2.974628e-04 1.717840e-02 0.0018 1.248259e-02 0.0027 #> C>A_CCT 3.147943e-05 3.767696e-02 0.0096 1.034012e-01 0.0056 #> C>A_GCA 6.535405e-03 1.287242e-01 0.0032 1.116124e-03 0.0001 #> C>A_GCC 1.293804e-03 1.609288e-02 0.0031 3.271429e-03 0.0038 #> C>A_GCG 1.283663e-03 9.271417e-03 0.0000 3.751613e-03 0.0003 #> C>A_GCT 3.103767e-03 7.201707e-02 0.0072 1.293719e-02 0.0023 #> C>A_TCA 1.824558e-03 6.708064e-02 0.0051 6.882997e-04 0.0001 #> C>A_TCC 1.286518e-03 4.186901e-02 0.0063 4.058229e-03 0.0005 #> C>A_TCG 2.172942e-03 1.516238e-02 0.0018 1.001102e-03 0.0000 #> C>A_TCT 5.012316e-03 1.178778e-01 0.0087 1.222910e-02 0.0004 #> C>G_ACA 1.661704e-03 1.516888e-03 0.0058 6.970411e-04 0.0005 #> C>G_ACC 1.626898e-03 2.498785e-03 0.0019 2.059310e-03 0.0008 #> C>G_ACG 2.580190e-05 2.614509e-03 0.0000 1.273496e-05 0.0000 #> C>G_ACT 1.328508e-03 3.983011e-03 0.0072 8.485871e-04 0.0018 #> C>G_CCA 1.924979e-03 4.584638e-04 0.0002 1.331626e-05 0.0001 #> C>G_CCC 7.093678e-04 3.654228e-03 0.0028 5.481447e-04 0.0000 #> C>G_CCG 3.517869e-06 5.405774e-03 0.0002 0.000000e+00 0.0000 #> C>G_CCT 9.537763e-04 5.519605e-03 0.0008 1.207306e-04 0.0003 #> C>G_GCA 1.296324e-03 9.238797e-04 0.0020 1.339769e-03 0.0004 #> C>G_GCC 2.607609e-04 6.486479e-04 0.0000 1.811151e-03 0.0042 #> C>G_GCG 4.377552e-06 5.428400e-04 0.0000 6.375380e-07 0.0000 #> C>G_GCT 1.820393e-03 1.376725e-03 0.0000 1.238264e-03 0.0004 #> C>G_TCA 3.926847e-04 1.802969e-03 0.0005 2.429847e-05 0.0002 #> C>G_TCC 6.556024e-04 7.863007e-03 0.0011 1.519986e-04 0.0003 #> C>G_TCG 1.364154e-05 1.513223e-03 0.0000 0.000000e+00 0.0000 #> C>G_TCT 2.852380e-03 3.567102e-03 0.0105 6.830600e-04 0.0003 #> C>T_ACA 9.350488e-03 3.825624e-03 0.0221 3.285805e-02 0.0051 #> C>T_ACC 4.224289e-03 2.465214e-03 0.0203 2.219605e-02 0.0062 #> C>T_ACG 9.229213e-03 8.463957e-03 0.0368 3.457201e-02 0.0256 #> C>T_ACT 5.735961e-03 5.605740e-03 0.0266 1.881956e-02 0.0030 #> C>T_CCA 2.126521e-02 9.767511e-03 0.0438 1.114519e-02 0.0034 #> C>T_CCC 3.847235e-03 5.654828e-03 0.0753 1.815275e-02 0.0091 #> C>T_CCG 1.317611e-02 1.618322e-02 0.0238 4.438494e-02 0.0318 #> C>T_CCT 9.648025e-03 5.153319e-03 0.1159 1.384714e-02 0.0040 #> C>T_GCA 2.068755e-03 2.703069e-03 0.0374 5.679395e-02 0.0163 #> C>T_GCC 3.254834e-04 4.199308e-03 0.0614 5.442986e-02 0.0392 #> C>T_GCG 7.511101e-03 1.189736e-02 0.0278 4.592689e-03 0.0019 #> C>T_GCT 9.256972e-04 1.913381e-03 0.0917 4.958086e-02 0.0166 #> C>T_TCA 1.610078e-02 1.492339e-02 0.0218 1.071032e-02 0.0064 #> C>T_TCC 1.677998e-02 9.962744e-03 0.0330 8.175510e-03 0.0086 #> C>T_TCG 1.627210e-02 1.154972e-02 0.0090 2.316390e-02 0.0126 #> C>T_TCT 1.982742e-02 5.398014e-03 0.0267 9.540087e-03 0.0064 #> T>A_ATA 6.130025e-04 3.037211e-03 0.0011 5.744014e-04 0.0083 #> T>A_ATC 1.878587e-03 8.111672e-04 0.0053 1.971462e-03 0.0292 #> T>A_ATG 1.087350e-03 4.503207e-03 0.0045 1.905866e-04 0.0027 #> T>A_ATT 2.045494e-03 2.736523e-03 0.0033 7.421104e-03 0.0043 #> T>A_CTA 3.007924e-05 4.123464e-04 0.0043 4.504236e-05 0.0000 #> T>A_CTC 1.022375e-02 2.491411e-03 0.0053 4.389056e-03 0.0037 #> T>A_CTG 4.467036e-03 5.523046e-03 0.0021 1.127836e-03 0.0025 #> T>A_CTT 3.124488e-02 3.313713e-03 0.0022 2.385541e-03 0.0010 #> T>A_GTA 8.545689e-06 1.875434e-03 0.0026 1.631298e-04 0.0000 #> T>A_GTC 2.573467e-03 1.510310e-03 0.0000 3.799180e-03 0.0142 #> T>A_GTG 3.538823e-03 1.505369e-03 0.0016 8.283337e-04 0.0031 #> T>A_GTT 3.879010e-03 3.611025e-03 0.0052 1.900747e-03 0.0041 #> T>A_TTA 6.988123e-04 4.663278e-03 0.0039 9.245480e-04 0.0027 #> T>A_TTC 2.579359e-03 2.578156e-03 0.0048 7.082068e-04 0.0045 #> T>A_TTG 2.113364e-05 2.016738e-03 0.0052 9.700313e-05 0.0000 #> T>A_TTT 3.883131e-03 2.818679e-03 0.0085 2.313489e-03 0.0008 #> T>C_ATA 2.697314e-03 2.933054e-03 0.0145 1.639506e-02 0.0265 #> T>C_ATC 8.078150e-03 1.513285e-03 0.0048 1.925179e-02 0.0165 #> T>C_ATG 4.432871e-03 3.329669e-03 0.0135 5.478492e-02 0.0224 #> T>C_ATT 3.140370e-03 5.491318e-03 0.0160 7.341270e-03 0.0189 #> T>C_CTA 7.427000e-03 1.921693e-04 0.0066 1.486770e-02 0.0219 #> T>C_CTC 3.965700e-02 3.050193e-03 0.0070 1.835616e-02 0.0100 #> T>C_CTG 2.860970e-02 2.596464e-03 0.0040 7.415056e-02 0.0211 #> T>C_CTT 1.018697e-01 1.310029e-03 0.0053 1.100112e-02 0.0204 #> T>C_GTA 1.140133e-05 5.291265e-04 0.0039 2.469317e-03 0.1426 #> T>C_GTC 9.657713e-03 2.279131e-03 0.0030 1.565633e-03 0.0665 #> T>C_GTG 4.654129e-03 5.871057e-03 0.0060 2.734176e-02 0.0884 #> T>C_GTT 8.149235e-03 4.771566e-03 0.0099 1.498265e-03 0.1003 #> T>C_TTA 1.708587e-03 3.023036e-04 0.0052 5.734230e-03 0.0389 #> T>C_TTC 1.107415e-02 6.260791e-03 0.0020 1.123425e-02 0.0313 #> T>C_TTG 5.932003e-03 1.541265e-03 0.0057 2.376761e-02 0.0249 #> T>C_TTT 7.208218e-03 1.357797e-03 0.0038 5.395186e-03 0.0274 #> T>G_ATA 5.313925e-05 3.861382e-04 0.0014 1.765291e-06 0.0000 #> T>G_ATC 6.468661e-03 1.254982e-03 0.0000 3.813879e-04 0.0031 #> T>G_ATG 3.481549e-03 2.369216e-03 0.0010 6.587581e-04 0.0016 #> T>G_ATT 3.092638e-02 3.386029e-04 0.0017 5.321252e-04 0.0018 #> T>G_CTA 9.146979e-05 6.100255e-05 0.0000 2.326408e-05 0.0000 #> T>G_CTC 1.981429e-02 2.015697e-03 0.0011 8.476495e-03 0.0005 #> T>G_CTG 1.344984e-02 5.311967e-03 0.0013 1.538378e-02 0.0004 #> T>G_CTT 2.614566e-01 2.341629e-03 0.0019 2.185395e-03 0.0032 #> T>G_GTA 3.919382e-05 1.341532e-03 0.0000 3.579149e-06 0.0000 #> T>G_GTC 9.078462e-03 9.204310e-07 0.0000 2.830575e-03 0.0006 #> T>G_GTG 4.782775e-03 9.695000e-03 0.0043 2.733219e-03 0.0004 #> T>G_GTT 6.349776e-02 2.890554e-03 0.0025 3.558559e-03 0.0008 #> T>G_TTA 1.334106e-04 3.631840e-05 0.0032 2.691470e-07 0.0000 #> T>G_TTC 9.613345e-03 3.233838e-03 0.0018 3.772344e-04 0.0018 #> T>G_TTG 4.522462e-03 7.546018e-04 0.0011 5.154216e-04 0.0003 #> T>G_TTT 5.804041e-02 2.126442e-03 0.0013 6.156567e-04 0.0003 #> Signature22 Signature23 Signature24 Signature25 Signature26 #> C>A_ACA 0.0015040704 4.533607e-04 2.864599e-02 0.0098967680 2.039773e-03 #> C>A_ACC 0.0024510110 3.668005e-04 2.021464e-02 0.0069989288 1.487162e-03 #> C>A_ACG 0.0000000000 0.000000e+00 2.047900e-02 0.0014484430 2.839456e-04 #> C>A_ACT 0.0009224525 0.000000e+00 2.460015e-02 0.0049665650 5.978656e-04 #> C>A_CCA 0.0045496929 1.647394e-04 6.355928e-02 0.0148329479 3.705850e-03 #> C>A_CCC 0.0037644739 7.368748e-04 3.375700e-02 0.0078221753 3.980723e-03 #> C>A_CCG 0.0009001633 1.639537e-04 2.242899e-02 0.0012769767 8.117420e-04 #> C>A_CCT 0.0044398462 7.227318e-04 2.008652e-02 0.0125636547 1.903843e-02 #> C>A_GCA 0.0012983702 3.499075e-04 5.467645e-02 0.0134652951 1.375312e-03 #> C>A_GCC 0.0018096222 5.683378e-04 1.099460e-01 0.0064682981 1.961639e-03 #> C>A_GCG 0.0003338381 1.494178e-04 4.652487e-02 0.0006581031 1.322966e-05 #> C>A_GCT 0.0005191482 0.000000e+00 5.042871e-02 0.0104730803 1.934996e-03 #> C>A_TCA 0.0040516346 2.071290e-03 3.145126e-02 0.0069381466 2.680062e-03 #> C>A_TCC 0.0027397709 6.964102e-04 6.253829e-02 0.0102466074 2.031644e-03 #> C>A_TCG 0.0005131511 9.939363e-05 1.280259e-02 0.0000000000 2.650717e-04 #> C>A_TCT 0.0036056509 2.074302e-04 3.029768e-02 0.0246257872 3.017187e-03 #> C>G_ACA 0.0005276440 0.000000e+00 1.199304e-02 0.0080325676 1.272881e-03 #> C>G_ACC 0.0000000000 0.000000e+00 8.425120e-03 0.0016359704 1.528195e-03 #> C>G_ACG 0.0000000000 0.000000e+00 0.000000e+00 0.0000000000 3.072463e-04 #> C>G_ACT 0.0002994547 0.000000e+00 3.881383e-03 0.0034284497 2.498252e-03 #> C>G_CCA 0.0005820177 1.990492e-04 1.347682e-02 0.0072007904 1.279106e-03 #> C>G_CCC 0.0008252996 2.837760e-04 1.610569e-02 0.0045984731 1.214977e-03 #> C>G_CCG 0.0003821146 0.000000e+00 7.974720e-04 0.0008237093 2.078326e-04 #> C>G_CCT 0.0017606459 1.957753e-04 1.038867e-02 0.0001963603 2.297026e-03 #> C>G_GCA 0.0000000000 0.000000e+00 4.945061e-03 0.0041696555 1.320607e-03 #> C>G_GCC 0.0000000000 1.375011e-04 9.369876e-03 0.0023928049 1.845501e-03 #> C>G_GCG 0.0002146959 0.000000e+00 5.625727e-03 0.0004181939 2.050608e-04 #> C>G_GCT 0.0005384388 0.000000e+00 3.055770e-03 0.0019940122 1.225533e-03 #> C>G_TCA 0.0002254906 2.306089e-04 1.022086e-02 0.0097987246 4.201897e-03 #> C>G_TCC 0.0006286950 1.657870e-04 7.578365e-03 0.0032665071 2.807762e-03 #> C>G_TCG 0.0003958080 0.000000e+00 1.592714e-03 0.0020574368 6.197000e-09 #> C>G_TCT 0.0002573751 4.389558e-04 6.100727e-03 0.0164009168 8.019383e-03 #> C>T_ACA 0.0031133897 1.976715e-02 6.315518e-03 0.0209876181 5.907232e-03 #> C>T_ACC 0.0015248603 8.188058e-02 3.844327e-03 0.0131412837 1.062646e-02 #> C>T_ACG 0.0036256412 9.248715e-03 3.110664e-03 0.0196598943 1.993032e-02 #> C>T_ACT 0.0000000000 3.320965e-02 3.420419e-03 0.0057285193 1.133453e-02 #> C>T_CCA 0.0077313495 6.057263e-02 6.035447e-03 0.0143339947 6.594445e-03 #> C>T_CCC 0.0071108505 1.863756e-01 0.000000e+00 0.0059366437 6.510632e-03 #> C>T_CCG 0.0055020310 1.514908e-02 2.924419e-03 0.0115593916 1.190494e-02 #> C>T_CCT 0.0041697772 1.560154e-01 3.971202e-03 0.0136325969 6.238556e-03 #> C>T_GCA 0.0019153709 5.328206e-02 2.367905e-02 0.0100381120 9.606515e-03 #> C>T_GCC 0.0032291335 1.629183e-01 1.591920e-02 0.0069538752 1.950743e-02 #> C>T_GCG 0.0033005989 1.304649e-02 1.264808e-02 0.0104683630 2.250272e-02 #> C>T_GCT 0.0011140596 1.075904e-01 1.812978e-02 0.0098238207 1.730747e-02 #> C>T_TCA 0.0020167217 1.455861e-02 2.657189e-02 0.0110775208 1.130329e-02 #> C>T_TCC 0.0019908342 4.351045e-02 1.205569e-02 0.0064487875 1.080753e-02 #> C>T_TCG 0.0014984731 2.752641e-03 5.363360e-03 0.0140834162 1.036433e-02 #> C>T_TCT 0.0011822265 2.432879e-02 5.532499e-03 0.0124185859 7.249145e-03 #> T>A_ATA 0.0496192297 0.000000e+00 1.166747e-03 0.0204305271 4.459340e-03 #> T>A_ATC 0.0116667405 0.000000e+00 1.517306e-05 0.0088925607 1.282224e-02 #> T>A_ATG 0.0679154542 2.374185e-04 6.332456e-03 0.0062419485 1.172344e-03 #> T>A_ATT 0.0145999176 0.000000e+00 4.967216e-06 0.0148508776 3.993138e-03 #> T>A_CTA 0.0868985455 5.945285e-04 2.766635e-03 0.0262963231 3.561423e-03 #> T>A_CTC 0.0537068468 0.000000e+00 2.694462e-03 0.0157998831 3.901611e-03 #> T>A_CTG 0.2132208666 1.731204e-04 6.911165e-03 0.0628606064 2.390304e-03 #> T>A_CTT 0.0618275075 4.578131e-04 2.915200e-03 0.0366223511 1.635923e-03 #> T>A_GTA 0.0537091457 0.000000e+00 2.225127e-03 0.0362178008 2.242887e-03 #> T>A_GTC 0.0094893967 1.832038e-04 4.853149e-03 0.0058471096 5.207287e-03 #> T>A_GTG 0.0502939024 0.000000e+00 1.957586e-04 0.0382411793 1.358122e-03 #> T>A_GTT 0.0106014572 0.000000e+00 0.000000e+00 0.0201679544 2.513113e-03 #> T>A_TTA 0.0408105028 0.000000e+00 0.000000e+00 0.0218303290 6.281453e-04 #> T>A_TTC 0.0255703958 0.000000e+00 7.994129e-03 0.0034056867 5.073754e-03 #> T>A_TTG 0.0698452181 2.315256e-04 1.120214e-02 0.0101915204 2.013839e-05 #> T>A_TTT 0.0235790618 0.000000e+00 2.705788e-04 0.0145275393 1.235538e-03 #> T>C_ATA 0.0168399309 1.068449e-03 4.726009e-03 0.0206632828 5.502865e-02 #> T>C_ATC 0.0011082624 2.215732e-04 6.279493e-04 0.0095024784 2.759460e-02 #> T>C_ATG 0.0049136164 4.988015e-04 2.723759e-03 0.0199114925 5.179104e-02 #> T>C_ATT 0.0026305239 3.132405e-04 7.122368e-03 0.0144883903 3.907224e-02 #> T>C_CTA 0.0040273463 0.000000e+00 1.848877e-03 0.0090280149 3.788938e-02 #> T>C_CTC 0.0013524439 0.000000e+00 4.453690e-03 0.0107716324 2.174073e-02 #> T>C_CTG 0.0027496661 3.207049e-04 0.000000e+00 0.0133506613 4.724010e-02 #> T>C_CTT 0.0023633535 0.000000e+00 1.597389e-03 0.0089610300 2.074062e-02 #> T>C_GTA 0.0042174541 2.511686e-04 1.269750e-03 0.0174898239 9.805282e-02 #> T>C_GTC 0.0000000000 5.382185e-04 6.710340e-03 0.0040456124 4.022636e-02 #> T>C_GTG 0.0014748845 0.000000e+00 2.776850e-04 0.0134022463 4.462070e-02 #> T>C_GTT 0.0015610427 9.957697e-04 4.238478e-03 0.0141596937 5.552807e-02 #> T>C_TTA 0.0048036697 0.000000e+00 1.682291e-03 0.0145150501 2.878968e-02 #> T>C_TTC 0.0009121575 2.306089e-04 2.344528e-03 0.0074060835 3.663949e-02 #> T>C_TTG 0.0017817357 2.395138e-04 4.812742e-04 0.0048925312 1.914369e-02 #> T>C_TTT 0.0000000000 0.000000e+00 3.581480e-04 0.0170147808 2.307169e-02 #> T>G_ATA 0.0016519986 0.000000e+00 0.000000e+00 0.0052816797 8.065343e-05 #> T>G_ATC 0.0000000000 0.000000e+00 1.463951e-03 0.0000000000 1.631712e-04 #> T>G_ATG 0.0010868728 0.000000e+00 8.476125e-04 0.0071364216 1.255080e-03 #> T>G_ATT 0.0000000000 0.000000e+00 1.075455e-03 0.0000000000 1.850383e-03 #> T>G_CTA 0.0011203565 0.000000e+00 0.000000e+00 0.0000000000 9.539626e-05 #> T>G_CTC 0.0010645836 1.901443e-04 2.185437e-03 0.0028864543 3.919455e-03 #> T>G_CTG 0.0041885681 0.000000e+00 1.139097e-04 0.0117694925 5.497357e-03 #> T>G_CTT 0.0016294096 2.108350e-04 2.533718e-03 0.0085508075 6.788719e-03 #> T>G_GTA 0.0000000000 0.000000e+00 0.000000e+00 0.0055462269 3.739323e-05 #> T>G_GTC 0.0000000000 0.000000e+00 1.073632e-03 0.0000000000 2.460705e-03 #> T>G_GTG 0.0018775892 1.871324e-04 2.924697e-03 0.0086852444 8.172016e-04 #> T>G_GTT 0.0000000000 0.000000e+00 8.250983e-04 0.0027685717 7.833561e-03 #> T>G_TTA 0.0016516988 0.000000e+00 0.000000e+00 0.0020814799 8.534935e-06 #> T>G_TTC 0.0000000000 0.000000e+00 0.000000e+00 0.0005789788 2.718510e-03 #> T>G_TTG 0.0025727520 2.475019e-04 1.360505e-03 0.0094291959 1.369161e-03 #> T>G_TTT 0.0000000000 0.000000e+00 6.951578e-05 0.0078696716 2.568077e-03 #> Signature27 Signature28 Signature29 Signature30 #> C>A_ACA 5.205627e-03 1.397439e-03 0.0699819873 0.0000000 #> C>A_ACC 4.738227e-03 9.171877e-04 0.0551523572 0.0000000 #> C>A_ACG 7.826979e-04 0.000000e+00 0.0178469840 0.0019673 #> C>A_ACT 2.718242e-03 5.134100e-04 0.0268047160 0.0000000 #> C>A_CCA 5.065073e-03 1.168516e-03 0.0514102117 0.0000000 #> C>A_CCC 2.234153e-03 3.342918e-04 0.0258256508 0.0000000 #> C>A_CCG 2.663122e-04 5.365200e-05 0.0144961833 0.0022624 #> C>A_CCT 3.100570e-03 1.866719e-04 0.0403550741 0.0000000 #> C>A_GCA 1.075587e-02 2.136629e-03 0.0780466101 0.0088530 #> C>A_GCC 1.244234e-02 4.292084e-04 0.0734609147 0.0093449 #> C>A_GCG 1.629628e-03 0.000000e+00 0.0173832969 0.0008853 #> C>A_GCT 7.412355e-03 1.318507e-03 0.0596024721 0.0081645 #> C>A_TCA 7.079285e-03 7.759028e-04 0.0268944065 0.0000000 #> C>A_TCC 6.268801e-03 8.292925e-04 0.0316081370 0.0000000 #> C>A_TCG 1.446403e-03 0.000000e+00 0.0125004682 0.0016722 #> C>A_TCT 9.806278e-03 1.998074e-03 0.0412071764 0.0000000 #> C>G_ACA 1.324163e-03 2.551950e-04 0.0093019711 0.0000000 #> C>G_ACC 1.771084e-03 2.688990e-04 0.0034790489 0.0000000 #> C>G_ACG 0.000000e+00 0.000000e+00 0.0001544335 0.0048200 #> C>G_ACT 1.322720e-03 3.076980e-04 0.0039767899 0.0000000 #> C>G_CCA 4.730649e-03 1.033661e-04 0.0026188632 0.0000000 #> C>G_CCC 1.261645e-03 1.443108e-04 0.0011115123 0.0000000 #> C>G_CCG 3.608566e-04 0.000000e+00 0.0015200470 0.0032461 #> C>G_CCT 2.680262e-04 2.909995e-04 0.0001397507 0.0000000 #> C>G_GCA 1.418166e-03 8.159141e-05 0.0002657599 0.0073775 #> C>G_GCC 1.346717e-03 1.052190e-04 0.0009450129 0.0065906 #> C>G_GCG 0.000000e+00 0.000000e+00 0.0000000000 0.0015739 #> C>G_GCT 4.560686e-03 1.596794e-04 0.0047967447 0.0000000 #> C>G_TCA 2.870434e-03 5.213704e-04 0.0008204449 0.0000000 #> C>G_TCC 3.107968e-03 6.673259e-04 0.0004441193 0.0000000 #> C>G_TCG 1.281041e-05 0.000000e+00 0.0001432972 0.0019673 #> C>G_TCT 2.130588e-03 1.245780e-03 0.0013698690 0.0000000 #> C>T_ACA 1.372329e-02 5.433792e-03 0.0051972213 0.0651190 #> C>T_ACC 5.424306e-03 1.815415e-03 0.0089764700 0.0543970 #> C>T_ACG 6.706429e-03 5.432039e-03 0.0316389964 0.0204604 #> C>T_ACT 4.475614e-03 1.629213e-03 0.0047696666 0.0219359 #> C>T_CCA 1.743848e-02 4.391533e-03 0.0091264718 0.0694472 #> C>T_CCC 7.144870e-03 2.647661e-03 0.0070676030 0.0638403 #> C>T_CCG 7.503562e-03 2.284564e-03 0.0198751804 0.0173126 #> C>T_CCT 7.148028e-03 2.423984e-03 0.0016340587 0.0342318 #> C>T_GCA 1.421531e-02 3.384241e-03 0.0116387930 0.0485934 #> C>T_GCC 2.014365e-02 1.687414e-03 0.0037817517 0.0494787 #> C>T_GCG 9.368468e-03 2.189309e-03 0.0196843880 0.0157387 #> C>T_GCT 7.589626e-03 1.043994e-03 0.0057613368 0.0188865 #> C>T_TCA 1.875778e-02 7.622258e-03 0.0120765831 0.0849892 #> C>T_TCC 7.989184e-03 5.116619e-03 0.0000000000 0.0903010 #> C>T_TCG 4.609131e-03 1.918028e-03 0.0158301968 0.0151485 #> C>T_TCT 1.188093e-02 6.193159e-03 0.0134621373 0.0455440 #> T>A_ATA 1.430764e-01 9.640309e-04 0.0000000000 0.0075743 #> T>A_ATC 1.464085e-03 3.365668e-03 0.0030495957 0.0037380 #> T>A_ATG 1.226281e-03 1.785754e-03 0.0039099820 0.0065906 #> T>A_ATT 2.535198e-03 5.653089e-03 0.0051055274 0.0093447 #> T>A_CTA 3.306010e-01 2.566580e-03 0.0017654475 0.0053118 #> T>A_CTC 2.813599e-03 1.961090e-02 0.0003833591 0.0067873 #> T>A_CTG 4.396857e-03 8.833600e-03 0.0035568452 0.0082628 #> T>A_CTT 5.430892e-03 1.094261e-02 0.0022327555 0.0000000 #> T>A_GTA 1.098519e-01 5.514608e-04 0.0029300981 0.0037380 #> T>A_GTC 2.345568e-05 3.163988e-03 0.0000000000 0.0033445 #> T>A_GTG 1.565937e-03 2.152847e-03 0.0005336324 0.0050167 #> T>A_GTT 0.000000e+00 2.007733e-03 0.0000000000 0.0063939 #> T>A_TTA 5.281389e-02 2.032376e-04 0.0011912074 0.0076726 #> T>A_TTC 4.709179e-05 1.018096e-02 0.0016826640 0.0064922 #> T>A_TTG 0.000000e+00 3.250427e-03 0.0024387560 0.0036396 #> T>A_TTT 1.929771e-03 1.649281e-02 0.0000000000 0.0000000 #> T>C_ATA 5.047301e-03 4.092747e-03 0.0101191812 0.0000000 #> T>C_ATC 1.845691e-03 7.880729e-03 0.0063496827 0.0087547 #> T>C_ATG 5.688814e-03 5.520834e-03 0.0146596103 0.0090498 #> T>C_ATT 2.592755e-03 3.232484e-03 0.0078924134 0.0000000 #> T>C_CTA 4.899079e-03 2.073800e-02 0.0000000000 0.0000000 #> T>C_CTC 5.724448e-03 4.328380e-02 0.0027749537 0.0000000 #> T>C_CTG 5.661479e-03 3.708826e-02 0.0069024147 0.0000000 #> T>C_CTT 3.900589e-03 5.052716e-03 0.0030414249 0.0000000 #> T>C_GTA 4.777380e-03 3.655048e-03 0.0070908038 0.0000000 #> T>C_GTC 1.964954e-03 7.071175e-03 0.0071113275 0.0065906 #> T>C_GTG 1.229168e-03 8.232238e-03 0.0056430636 0.0078694 #> T>C_GTT 3.747225e-03 4.078845e-04 0.0112376743 0.0084596 #> T>C_TTA 1.721015e-03 9.929552e-03 0.0114986660 0.0000000 #> T>C_TTC 3.489213e-03 2.901056e-02 0.0035842150 0.0091481 #> T>C_TTG 1.152847e-03 1.568322e-02 0.0016942967 0.0060004 #> T>C_TTT 1.527957e-03 1.729156e-02 0.0037997058 0.0000000 #> T>G_ATA 1.136337e-03 6.364676e-03 0.0000000000 0.0053118 #> T>G_ATC 9.589764e-04 1.661091e-02 0.0000000000 0.0024592 #> T>G_ATG 6.766061e-05 6.592842e-03 0.0029251714 0.0062955 #> T>G_ATT 2.560277e-04 8.639290e-02 0.0000000000 0.0095416 #> T>G_CTA 0.000000e+00 9.589842e-03 0.0011168548 0.0046233 #> T>G_CTC 3.812450e-04 3.391322e-02 0.0000000000 0.0060004 #> T>G_CTG 4.032572e-04 1.851648e-02 0.0021696933 0.0073775 #> T>G_CTT 1.439096e-03 1.189671e-01 0.0011436633 0.0091481 #> T>G_GTA 0.000000e+00 0.000000e+00 0.0000000000 0.0032461 #> T>G_GTC 5.079056e-05 0.000000e+00 0.0000000000 0.0018690 #> T>G_GTG 4.742919e-03 4.217808e-03 0.0036405938 0.0033445 #> T>G_GTT 2.298476e-03 3.164900e-02 0.0061810238 0.0056069 #> T>G_TTA 1.189022e-03 9.389659e-03 0.0000000000 0.0086563 #> T>G_TTC 2.802954e-04 3.011708e-02 0.0000000000 0.0043282 #> T>G_TTG 2.353056e-03 1.269875e-02 0.0003536960 0.0082628 #> T>G_TTT 1.395613e-04 2.336598e-01 0.0061048341 0.0000000 #> #> Slot "exposures": #> TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08 #> Signature1 2.656984e-15 6.833284e-15 #> Signature2 5.819272e-15 4.099963e-15 #> Signature3 1.164181e+01 2.298342e+01 #> Signature4 1.102129e+01 4.917963e+00 #> Signature5 4.071420e+00 7.399814e+00 #> Signature6 3.977903e-15 6.621970e-15 #> Signature7 2.260251e-01 2.583266e-01 #> Signature8 2.065822e+00 2.986695e+00 #> Signature9 4.405151e-15 7.319428e-15 #> Signature10 6.311509e-15 3.002818e-15 #> Signature11 4.142279e+00 4.572896e+00 #> Signature12 5.216801e-15 6.681923e-15 #> Signature13 2.618237e-15 4.351530e-15 #> Signature14 6.889633e-15 5.267841e-15 #> Signature15 5.004167e-15 6.099663e-15 #> Signature16 3.010727e+00 3.679865e+00 #> Signature17 4.314209e-15 1.064661e-14 #> Signature18 1.799609e-01 4.565175e-02 #> Signature19 2.892433e+00 3.743653e+00 #> Signature20 6.805754e-15 5.689277e-15 #> Signature21 3.374094e-15 7.025231e-15 #> Signature22 8.595197e-15 8.668449e-15 #> Signature23 2.351449e+00 1.514705e+00 #> Signature24 2.505777e-08 1.984885e-08 #> Signature25 5.317848e-15 6.818315e-15 #> Signature26 5.162128e-15 7.404232e-15 #> Signature27 2.191238e-14 5.669122e-15 #> Signature28 3.079350e-15 6.876398e-15 #> Signature29 6.008364e-15 5.360469e-15 #> Signature30 5.396785e+00 5.897013e+00 #> TCGA-94-7557-01A-11D-2122-08 TCGA-97-7938-01A-11D-2167-08 #> Signature1 2.184220e-15 3.074818e-15 #> Signature2 4.518475e-15 8.863752e-15 #> Signature3 1.010209e+01 2.852077e+01 #> Signature4 1.861367e+00 3.817717e+01 #> Signature5 3.027034e+00 5.118505e+00 #> Signature6 3.424647e-15 3.160088e-15 #> Signature7 3.261625e-01 6.845052e-01 #> Signature8 5.190695e-01 5.893436e+00 #> Signature9 2.978810e-15 5.055188e-15 #> Signature10 1.208575e-15 4.108724e-15 #> Signature11 3.916310e+00 4.597603e+00 #> Signature12 4.462341e-15 4.947791e-15 #> Signature13 5.869743e-15 9.397808e-15 #> Signature14 3.985472e-15 4.956062e-15 #> Signature15 2.993019e-15 3.207005e-15 #> Signature16 2.316748e+00 3.284425e+00 #> Signature17 3.146035e-15 5.218518e-15 #> Signature18 8.396905e-02 1.707545e+01 #> Signature19 2.483787e+00 3.425830e+00 #> Signature20 5.450314e-15 4.710579e-15 #> Signature21 2.931321e-15 2.483268e-15 #> Signature22 8.530922e-16 6.791149e-15 #> Signature23 1.805193e+00 1.611301e+00 #> Signature24 1.914601e-08 2.716005e-08 #> Signature25 2.932039e-15 6.345906e-15 #> Signature26 4.654500e-15 3.771905e-15 #> Signature27 1.647638e-15 5.949028e-15 #> Signature28 9.802668e-16 2.681727e-15 #> Signature29 4.614064e-15 7.013223e-15 #> Signature30 2.558266e+00 8.611001e+00 #> TCGA-EE-A3J5-06A-11D-A20D-08 TCGA-ER-A197-06A-32D-A197-08 #> Signature1 6.062986e-15 1.943897e-15 #> Signature2 5.545187e-15 4.271297e-16 #> Signature3 5.630218e+00 1.768561e+00 #> Signature4 9.475169e-01 9.530666e-01 #> Signature5 6.936536e+00 1.650218e+00 #> Signature6 6.002546e-15 2.726297e-15 #> Signature7 9.275296e-01 3.094558e-02 #> Signature8 8.697372e-01 3.542505e-01 #> Signature9 5.844267e-15 3.083823e-15 #> Signature10 2.010366e-15 7.604843e-15 #> Signature11 3.341182e+01 1.425527e+00 #> Signature12 8.994756e-15 5.123088e-15 #> Signature13 1.193978e-15 4.918276e-16 #> Signature14 4.898787e-15 3.319122e-15 #> Signature15 4.809574e-15 4.216624e-15 #> Signature16 4.457366e+00 1.181661e+00 #> Signature17 6.190170e-15 3.769734e-15 #> Signature18 3.208217e-02 3.066523e-02 #> Signature19 1.553891e+01 9.311211e-01 #> Signature20 6.303707e-15 2.500756e-15 #> Signature21 6.627491e-15 9.017566e-15 #> Signature22 4.973909e-15 1.218108e-14 #> Signature23 2.038665e+01 1.533098e+00 #> Signature24 1.093629e-08 6.326184e-09 #> Signature25 5.869328e-15 7.235605e-15 #> Signature26 6.649818e-15 7.320733e-15 #> Signature27 2.547754e-15 1.122902e-14 #> Signature28 3.567551e-15 6.793139e-16 #> Signature29 3.599138e-15 1.933472e-15 #> Signature30 3.286163e+01 1.140887e+00 #> TCGA-ER-A19O-06A-11D-A197-08 #> Signature1 3.246008e-15 #> Signature2 6.797914e-15 #> Signature3 2.724068e+00 #> Signature4 4.918150e-01 #> Signature5 1.526728e+00 #> Signature6 3.389679e-15 #> Signature7 7.922689e+00 #> Signature8 3.787067e-01 #> Signature9 3.905686e-15 #> Signature10 4.110702e-15 #> Signature11 1.181500e+01 #> Signature12 2.402008e-15 #> Signature13 1.282848e-15 #> Signature14 3.563109e-15 #> Signature15 2.929035e-15 #> Signature16 1.077522e+00 #> Signature17 3.085181e-15 #> Signature18 1.134420e-02 #> Signature19 3.376605e+00 #> Signature20 3.382013e-15 #> Signature21 1.870559e-15 #> Signature22 3.474234e-15 #> Signature23 5.308609e+00 #> Signature24 5.721853e-09 #> Signature25 3.607676e-15 #> Signature26 1.989851e-15 #> Signature27 2.014826e-15 #> Signature28 2.735823e-15 #> Signature29 1.135740e-15 #> Signature30 1.636692e+01 #> #> Slot "table_name": #> [1] "SBS96" #> #> Slot "algorithm": #> [1] "posterior_LDA" #> #> Slot "musica": #> An object of class "musica" #> Slot "variants": #> chr start end ref alt sample #> 1: chr1 11020563 11020563 C A TCGA-94-7557-01A-11D-2122-08 #> 2: chr1 43430030 43430030 G T TCGA-94-7557-01A-11D-2122-08 #> 3: chr1 58682403 58682403 A G TCGA-94-7557-01A-11D-2122-08 #> 4: chr1 109508295 109508295 C G TCGA-94-7557-01A-11D-2122-08 #> 5: chr1 156384826 156384826 A C TCGA-94-7557-01A-11D-2122-08 #> --- #> 907: chr19 54885292 54885292 G A TCGA-ER-A19O-06A-11D-A197-08 #> 908: chr20 49374328 49374328 A T TCGA-ER-A19O-06A-11D-A197-08 #> 909: chrX 73213768 73213768 T G TCGA-ER-A19O-06A-11D-A197-08 #> 910: chrX 101292834 101292834 G A TCGA-ER-A19O-06A-11D-A197-08 #> 911: chrX 107526690 107526690 C T TCGA-ER-A19O-06A-11D-A197-08 #> Variant_Type #> 1: SBS #> 2: SBS #> 3: SBS #> 4: SBS #> 5: SBS #> --- #> 907: SBS #> 908: SBS #> 909: SBS #> 910: SBS #> 911: SBS #> #> Slot "count_tables": #> $SBS96 #> Count_Table: SBS96 #> Motifs: 96 #> Samples: 7 #> #> **Annotations: #> motif mutation context #> C>A_ACA C>A_ACA C>A ACA #> C>A_ACC C>A_ACC C>A ACC #> C>A_ACG C>A_ACG C>A ACG #> C>A_ACT C>A_ACT C>A ACT #> C>A_CCA C>A_CCA C>A CCA #> C>A_CCC C>A_CCC C>A CCC #> 7 ... ... ... #> #> **Features: #> mutation #> 1 C>A_CCG #> 2 C>A_GCA #> 3 T>C_ATG #> 4 C>G_TGC #> 5 T>G_AGC #> 6 C>G_CCT #> 7 ... #> #> **Types: #> SBS #> #> **Color Variable: #> mutation #> #> **Color Mapping: #> #5ABCEBFF #> #050708FF #> #D33C32FF #> #CBCACBFF #> #ABCD72FF #> #E7C9C6FF #> #> **Descriptions: #> Single Base Substitution table with one base upstream and downstream #> #> #> Slot "sample_annotations": #> Samples Tumor_Subtypes #> 1: TCGA-94-7557-01A-11D-2122-08 Lung #> 2: TCGA-56-7582-01A-11D-2042-08 Lung #> 3: TCGA-77-7335-01A-11D-2042-08 Lung #> 4: TCGA-97-7938-01A-11D-2167-08 Lung #> 5: TCGA-EE-A3J5-06A-11D-A20D-08 Breast #> 6: TCGA-ER-A197-06A-32D-A197-08 Breast #> 7: TCGA-ER-A19O-06A-11D-A197-08 Breast #> #> #> Slot "umap": #> <0 x 0 matrix> #>