R/discovery_prediction.R
auto_predict_grid.RdAutomatic filtering of signatures for exposure prediction gridded across specific annotation
auto_predict_grid( musica, table_name, signature_res, algorithm, sample_annotation = NULL, min_exists = 0.05, proportion_samples = 0.25, rare_exposure = 0.4, verbose = TRUE, combine_res = TRUE )
| musica | Input samples to predit signature weights |
|---|---|
| table_name | Name of table used for posterior prediction (e.g. SBS96) |
| signature_res | Signatures to automatically subset from for prediction |
| algorithm | Algorithm to use for prediction. Choose from "lda_posterior", decompTumor2Sig, and deconstructSigs |
| sample_annotation | Annotation to grid across, if none given, prediction subsetting on all samples together |
| min_exists | Threshold to consider a signature active in a sample |
| proportion_samples | Threshold of samples to consider a signature active in the cohort |
| rare_exposure | A sample will be considered active in the cohort if at least one sample has more than this threshold proportion |
| verbose | Print current annotation value being predicted on |
| combine_res | Automatically combines a list of annotation results into a single result object with zero exposure values for signatures not found in a given annotation's set of samples |
A list of results, one per unique annotation value, if no annotation value is given, returns a single result for all samples, or combines into a single result if combines_res = TRUE
data(musica_annot) data(cosmic_v2_sigs) auto_predict_grid(musica = musica_annot, table_name = "SBS96", signature_res = cosmic_v2_sigs, algorithm = "lda", sample_annotation = "Tumor_Subtypes") #> Lung #> Breast #> An object of class "musica_result" #> Slot "signatures": #> Signature1 Signature13 Signature18 Signature20 Signature21 #> C>A_ACA 1.109833e-02 3.347572e-04 5.053642e-02 1.179962e-03 0.0001 #> C>A_ACC 9.149341e-03 6.487361e-04 1.093982e-02 2.211505e-03 0.0007 #> C>A_ACG 1.490070e-03 3.814459e-05 2.288073e-03 1.616910e-07 0.0000 #> C>A_ACT 6.233885e-03 8.466585e-04 1.942409e-02 3.008010e-03 0.0006 #> C>A_CCA 6.595870e-03 1.710090e-03 8.876811e-02 1.737711e-02 0.0020 #> C>A_CCC 7.342368e-03 1.159257e-03 2.064139e-02 3.650246e-02 0.0014 #> C>A_CCG 8.928404e-04 2.441665e-04 1.717840e-02 1.248259e-02 0.0027 #> C>A_CCT 7.186582e-03 1.256768e-03 3.767696e-02 1.034012e-01 0.0056 #> C>A_GCA 8.232604e-03 1.321096e-04 1.287242e-01 1.116124e-03 0.0001 #> C>A_GCC 5.758021e-03 7.542440e-04 1.609288e-02 3.271429e-03 0.0038 #> C>A_GCG 6.163352e-04 9.682078e-05 9.271417e-03 3.751613e-03 0.0003 #> C>A_GCT 4.459080e-03 5.511037e-04 7.201707e-02 1.293719e-02 0.0023 #> C>A_TCA 1.225006e-02 4.816605e-02 6.708064e-02 6.882997e-04 0.0001 #> C>A_TCC 1.116223e-02 1.732956e-02 4.186901e-02 4.058229e-03 0.0005 #> C>A_TCG 2.275496e-03 2.293157e-03 1.516238e-02 1.001102e-03 0.0000 #> C>A_TCT 1.525910e-02 1.863458e-02 1.178778e-01 1.222910e-02 0.0004 #> C>G_ACA 1.801068e-03 3.775165e-03 1.516888e-03 6.970411e-04 0.0005 #> C>G_ACC 2.580909e-03 9.208248e-04 2.498785e-03 2.059310e-03 0.0008 #> C>G_ACG 5.925480e-04 1.989049e-05 2.614509e-03 1.273496e-05 0.0000 #> C>G_ACT 2.963986e-03 3.860632e-03 3.983011e-03 8.485871e-04 0.0018 #> C>G_CCA 1.284983e-03 5.333651e-03 4.584638e-04 1.331626e-05 0.0001 #> C>G_CCC 7.021348e-04 9.123035e-04 3.654228e-03 5.481447e-04 0.0000 #> C>G_CCG 5.062896e-04 2.854673e-04 5.405774e-03 0.000000e+00 0.0000 #> C>G_CCT 1.381543e-03 6.383098e-03 5.519605e-03 1.207306e-04 0.0003 #> C>G_GCA 6.021227e-04 1.349420e-03 9.238797e-04 1.339769e-03 0.0004 #> C>G_GCC 2.393352e-03 7.888077e-04 6.486479e-04 1.811151e-03 0.0042 #> C>G_GCG 2.485340e-07 8.179121e-05 5.428400e-04 6.375380e-07 0.0000 #> C>G_GCT 8.900807e-04 2.680123e-03 1.376725e-03 1.238264e-03 0.0004 #> C>G_TCA 1.874853e-03 2.802349e-01 1.802969e-03 2.429847e-05 0.0002 #> C>G_TCC 2.067419e-03 6.388529e-02 7.863007e-03 1.519986e-04 0.0003 #> C>G_TCG 3.048970e-04 9.528486e-03 1.513223e-03 0.000000e+00 0.0000 #> C>G_TCT 3.151574e-03 3.302255e-01 3.567102e-03 6.830600e-04 0.0003 #> C>T_ACA 2.951453e-02 1.480181e-03 3.825624e-03 3.285805e-02 0.0051 #> C>T_ACC 1.432275e-02 4.050871e-05 2.465214e-03 2.219605e-02 0.0062 #> C>T_ACG 1.716469e-01 3.165947e-04 8.463957e-03 3.457201e-02 0.0256 #> C>T_ACT 1.262376e-02 0.000000e+00 5.605740e-03 1.881956e-02 0.0030 #> C>T_CCA 2.089645e-02 3.647278e-03 9.767511e-03 1.114519e-02 0.0034 #> C>T_CCC 1.850170e-02 1.004229e-03 5.654828e-03 1.815275e-02 0.0091 #> C>T_CCG 9.557722e-02 1.292021e-04 1.618322e-02 4.438494e-02 0.0318 #> C>T_CCT 1.711331e-02 6.117700e-04 5.153319e-03 1.384714e-02 0.0040 #> C>T_GCA 2.494381e-02 2.934138e-03 2.703069e-03 5.679395e-02 0.0163 #> C>T_GCC 2.716149e-02 2.515171e-03 4.199308e-03 5.442986e-02 0.0392 #> C>T_GCG 1.035708e-01 3.205265e-03 1.189736e-02 4.592689e-03 0.0019 #> C>T_GCT 1.768985e-02 1.687731e-03 1.913381e-03 4.958086e-02 0.0166 #> C>T_TCA 1.449210e-02 1.138421e-01 1.492339e-02 1.071032e-02 0.0064 #> C>T_TCC 1.768078e-02 1.502484e-02 9.962744e-03 8.175510e-03 0.0086 #> C>T_TCG 7.600222e-02 6.102098e-03 1.154972e-02 2.316390e-02 0.0126 #> C>T_TCT 1.376170e-02 2.814066e-02 5.398014e-03 9.540087e-03 0.0064 #> T>A_ATA 4.021520e-03 1.243618e-03 3.037211e-03 5.744014e-04 0.0083 #> T>A_ATC 2.371144e-03 1.060002e-03 8.111672e-04 1.971462e-03 0.0292 #> T>A_ATG 2.810910e-03 1.025544e-04 4.503207e-03 1.905866e-04 0.0027 #> T>A_ATT 8.360909e-03 9.718121e-04 2.736523e-03 7.421104e-03 0.0043 #> T>A_CTA 1.182587e-03 2.851590e-04 4.123464e-04 4.504236e-05 0.0000 #> T>A_CTC 1.903167e-03 2.222873e-04 2.491411e-03 4.389056e-03 0.0037 #> T>A_CTG 1.487961e-03 2.869518e-04 5.523046e-03 1.127836e-03 0.0025 #> T>A_CTT 2.179344e-03 8.004460e-07 3.313713e-03 2.385541e-03 0.0010 #> T>A_GTA 6.892894e-04 1.379604e-04 1.875434e-03 1.631298e-04 0.0000 #> T>A_GTC 5.524095e-04 2.528674e-04 1.510310e-03 3.799180e-03 0.0142 #> T>A_GTG 1.200229e-03 1.535175e-04 1.505369e-03 8.283337e-04 0.0031 #> T>A_GTT 2.107137e-03 1.227456e-04 3.611025e-03 1.900747e-03 0.0041 #> T>A_TTA 5.600155e-03 4.032613e-04 4.663278e-03 9.245480e-04 0.0027 #> T>A_TTC 1.999079e-03 7.718133e-04 2.578156e-03 7.082068e-04 0.0045 #> T>A_TTG 1.090066e-03 2.451942e-04 2.016738e-03 9.700313e-05 0.0000 #> T>A_TTT 3.981023e-03 1.603460e-04 2.818679e-03 2.313489e-03 0.0008 #> T>C_ATA 1.391577e-02 5.494542e-04 2.933054e-03 1.639506e-02 0.0265 #> T>C_ATC 6.274961e-03 1.455067e-04 1.513285e-03 1.925179e-02 0.0165 #> T>C_ATG 1.013764e-02 2.791780e-04 3.329669e-03 5.478492e-02 0.0224 #> T>C_ATT 9.256316e-03 2.674614e-04 5.491318e-03 7.341270e-03 0.0189 #> T>C_CTA 4.176675e-03 4.275147e-05 1.921693e-04 1.486770e-02 0.0219 #> T>C_CTC 5.252593e-03 4.330754e-05 3.050193e-03 1.835616e-02 0.0100 #> T>C_CTG 7.013225e-03 5.427253e-05 2.596464e-03 7.415056e-02 0.0211 #> T>C_CTT 6.713813e-03 7.639440e-07 1.310029e-03 1.100112e-02 0.0204 #> T>C_GTA 1.124784e-02 1.054081e-03 5.291265e-04 2.469317e-03 0.1426 #> T>C_GTC 6.999724e-03 5.298997e-04 2.279131e-03 1.565633e-03 0.0665 #> T>C_GTG 4.977593e-03 6.300957e-04 5.871057e-03 2.734176e-02 0.0884 #> T>C_GTT 1.066741e-02 6.761879e-04 4.771566e-03 1.498265e-03 0.1003 #> T>C_TTA 8.073616e-03 7.840561e-04 3.023036e-04 5.734230e-03 0.0389 #> T>C_TTC 4.857381e-03 1.329749e-04 6.260791e-03 1.123425e-02 0.0313 #> T>C_TTG 8.325454e-03 3.740240e-05 1.541265e-03 2.376761e-02 0.0249 #> T>C_TTT 6.257106e-03 1.797028e-04 1.357797e-03 5.395186e-03 0.0274 #> T>G_ATA 1.587636e-03 3.861998e-04 3.861382e-04 1.765291e-06 0.0000 #> T>G_ATC 1.784091e-03 1.123832e-04 1.254982e-03 3.813879e-04 0.0031 #> T>G_ATG 1.385831e-03 3.600070e-05 2.369216e-03 6.587581e-04 0.0016 #> T>G_ATT 3.158539e-03 1.924938e-04 3.386029e-04 5.321252e-04 0.0018 #> T>G_CTA 3.026912e-04 1.509421e-05 6.100255e-05 2.326408e-05 0.0000 #> T>G_CTC 2.098502e-03 1.476248e-04 2.015697e-03 8.476495e-03 0.0005 #> T>G_CTG 1.599549e-03 4.598730e-05 5.311967e-03 1.538378e-02 0.0004 #> T>G_CTT 2.758538e-03 4.637147e-04 2.341629e-03 2.185395e-03 0.0032 #> T>G_GTA 9.904500e-05 1.848986e-05 1.341532e-03 3.579149e-06 0.0000 #> T>G_GTC 2.023656e-04 9.337351e-05 9.204310e-07 2.830575e-03 0.0006 #> T>G_GTG 1.188353e-03 1.057919e-05 9.695000e-03 2.733219e-03 0.0004 #> T>G_GTT 8.007233e-04 5.374121e-05 2.890554e-03 3.558559e-03 0.0008 #> T>G_TTA 1.397554e-03 5.465818e-04 3.631840e-05 2.691470e-07 0.0000 #> T>G_TTC 1.291737e-03 2.353471e-04 3.233838e-03 3.772344e-04 0.0018 #> T>G_TTG 2.031077e-03 4.790220e-07 7.546018e-04 5.154216e-04 0.0003 #> T>G_TTT 4.030128e-03 6.705883e-04 2.126442e-03 6.156567e-04 0.0003 #> Signature22 Signature24 Signature3 Signature30 Signature4 #> C>A_ACA 0.0015040704 2.864599e-02 0.0221723068 0.0000000 0.0365 #> C>A_ACC 0.0024510110 2.021464e-02 0.0178716754 0.0000000 0.0309 #> C>A_ACG 0.0000000000 2.047900e-02 0.0021383396 0.0019673 0.0183 #> C>A_ACT 0.0009224525 2.460015e-02 0.0162651456 0.0000000 0.0243 #> C>A_CCA 0.0045496929 6.355928e-02 0.0187817256 0.0000000 0.0461 #> C>A_CCC 0.0037644739 3.375700e-02 0.0157604578 0.0000000 0.0614 #> C>A_CCG 0.0009001633 2.242899e-02 0.0019633898 0.0022624 0.0088 #> C>A_CCT 0.0044398462 2.008652e-02 0.0147228611 0.0000000 0.0432 #> C>A_GCA 0.0012983702 5.467645e-02 0.0096965397 0.0088530 0.0376 #> C>A_GCC 0.0018096222 1.099460e-01 0.0108433411 0.0093449 0.0399 #> C>A_GCG 0.0003338381 4.652487e-02 0.0009291405 0.0008853 0.0227 #> C>A_GCT 0.0005191482 5.042871e-02 0.0122153826 0.0081645 0.0258 #> C>A_TCA 0.0040516346 3.145126e-02 0.0116532249 0.0000000 0.0330 #> C>A_TCC 0.0027397709 6.253829e-02 0.0166067750 0.0000000 0.0538 #> C>A_TCG 0.0005131511 1.280259e-02 0.0013572394 0.0016722 0.0104 #> C>A_TCT 0.0036056509 3.029768e-02 0.0163280760 0.0000000 0.0370 #> C>G_ACA 0.0005276440 1.199304e-02 0.0240026152 0.0000000 0.0097 #> C>G_ACC 0.0000000000 8.425120e-03 0.0121603037 0.0000000 0.0054 #> C>G_ACG 0.0000000000 0.000000e+00 0.0052754195 0.0048200 0.0031 #> C>G_ACT 0.0002994547 3.881383e-03 0.0232776563 0.0000000 0.0054 #> C>G_CCA 0.0005820177 1.347682e-02 0.0168325720 0.0000000 0.0105 #> C>G_CCC 0.0008252996 1.610569e-02 0.0135314415 0.0000000 0.0097 #> C>G_CCG 0.0003821146 7.974720e-04 0.0041764575 0.0032461 0.0063 #> C>G_CCT 0.0017606459 1.038867e-02 0.0240463904 0.0000000 0.0094 #> C>G_GCA 0.0000000000 4.945061e-03 0.0119168446 0.0073775 0.0070 #> C>G_GCC 0.0000000000 9.369876e-03 0.0098236534 0.0065906 0.0091 #> C>G_GCG 0.0002146959 5.625727e-03 0.0016710543 0.0015739 0.0062 #> C>G_GCT 0.0005384388 3.055770e-03 0.0179143343 0.0000000 0.0060 #> C>G_TCA 0.0002254906 1.022086e-02 0.0160414054 0.0000000 0.0032 #> C>G_TCC 0.0006286950 7.578365e-03 0.0201499204 0.0000000 0.0105 #> C>G_TCG 0.0003958080 1.592714e-03 0.0025279109 0.0019673 0.0031 #> C>G_TCT 0.0002573751 6.100727e-03 0.0326736408 0.0000000 0.0050 #> C>T_ACA 0.0031133897 6.315518e-03 0.0178721707 0.0651190 0.0120 #> C>T_ACC 0.0015248603 3.844327e-03 0.0088960343 0.0543970 0.0075 #> C>T_ACG 0.0036256412 3.110664e-03 0.0035727083 0.0204604 0.0028 #> C>T_ACT 0.0000000000 3.420419e-03 0.0147976122 0.0219359 0.0059 #> C>T_CCA 0.0077313495 6.035447e-03 0.0143950595 0.0694472 0.0210 #> C>T_CCC 0.0071108505 0.000000e+00 0.0085447812 0.0638403 0.0144 #> C>T_CCG 0.0055020310 2.924419e-03 0.0035184658 0.0173126 0.0076 #> C>T_CCT 0.0041697772 3.971202e-03 0.0160755457 0.0342318 0.0201 #> C>T_GCA 0.0019153709 2.367905e-02 0.0161272733 0.0485934 0.0087 #> C>T_GCC 0.0032291335 1.591920e-02 0.0082086324 0.0494787 0.0080 #> C>T_GCG 0.0033005989 1.264808e-02 0.0012129229 0.0157387 0.0023 #> C>T_GCT 0.0011140596 1.812978e-02 0.0106116492 0.0188865 0.0082 #> C>T_TCA 0.0020167217 2.657189e-02 0.0088802091 0.0849892 0.0035 #> C>T_TCC 0.0019908342 1.205569e-02 0.0135295728 0.0903010 0.0070 #> C>T_TCG 0.0014984731 5.363360e-03 0.0017054089 0.0151485 0.0011 #> C>T_TCT 0.0011822265 5.532499e-03 0.0103044169 0.0455440 0.0077 #> T>A_ATA 0.0496192297 1.166747e-03 0.0084285636 0.0075743 0.0048 #> T>A_ATC 0.0116667405 1.517306e-05 0.0073730967 0.0037380 0.0039 #> T>A_ATG 0.0679154542 6.332456e-03 0.0073573000 0.0065906 0.0100 #> T>A_ATT 0.0145999176 4.967216e-06 0.0087539390 0.0093447 0.0030 #> T>A_CTA 0.0868985455 2.766635e-03 0.0075713203 0.0053118 0.0075 #> T>A_CTC 0.0537068468 2.694462e-03 0.0127254635 0.0067873 0.0111 #> T>A_CTG 0.2132208666 6.911165e-03 0.0115085619 0.0082628 0.0342 #> T>A_CTT 0.0618275075 2.915200e-03 0.0164561777 0.0000000 0.0115 #> T>A_GTA 0.0537091457 2.225127e-03 0.0044347826 0.0037380 0.0069 #> T>A_GTC 0.0094893967 4.853149e-03 0.0056154324 0.0033445 0.0052 #> T>A_GTG 0.0502939024 1.957586e-04 0.0080701365 0.0050167 0.0133 #> T>A_GTT 0.0106014572 0.000000e+00 0.0086791217 0.0063939 0.0045 #> T>A_TTA 0.0408105028 0.000000e+00 0.0071326814 0.0076726 0.0045 #> T>A_TTC 0.0255703958 7.994129e-03 0.0091027978 0.0064922 0.0046 #> T>A_TTG 0.0698452181 1.120214e-02 0.0065658630 0.0036396 0.0082 #> T>A_TTT 0.0235790618 2.705788e-04 0.0147121354 0.0000000 0.0045 #> T>C_ATA 0.0168399309 4.726009e-03 0.0130357094 0.0000000 0.0084 #> T>C_ATC 0.0011082624 6.279493e-04 0.0091862897 0.0087547 0.0020 #> T>C_ATG 0.0049136164 2.723759e-03 0.0117169201 0.0090498 0.0081 #> T>C_ATT 0.0026305239 7.122368e-03 0.0169788708 0.0000000 0.0036 #> T>C_CTA 0.0040273463 1.848877e-03 0.0078950126 0.0000000 0.0052 #> T>C_CTC 0.0013524439 4.453690e-03 0.0144311704 0.0000000 0.0026 #> T>C_CTG 0.0027496661 0.000000e+00 0.0084229721 0.0000000 0.0100 #> T>C_CTT 0.0023633535 1.597389e-03 0.0119324305 0.0000000 0.0054 #> T>C_GTA 0.0042174541 1.269750e-03 0.0068500556 0.0000000 0.0061 #> T>C_GTC 0.0000000000 6.710340e-03 0.0062607490 0.0065906 0.0016 #> T>C_GTG 0.0014748845 2.776850e-04 0.0060987630 0.0078694 0.0042 #> T>C_GTT 0.0015610427 4.238478e-03 0.0075093439 0.0084596 0.0024 #> T>C_TTA 0.0048036697 1.682291e-03 0.0091154951 0.0000000 0.0028 #> T>C_TTC 0.0009121575 2.344528e-03 0.0109537909 0.0091481 0.0016 #> T>C_TTG 0.0017817357 4.812742e-04 0.0061130332 0.0060004 0.0036 #> T>C_TTT 0.0000000000 3.581480e-04 0.0107743363 0.0000000 0.0022 #> T>G_ATA 0.0016519986 0.000000e+00 0.0023513681 0.0053118 0.0000 #> T>G_ATC 0.0000000000 1.463951e-03 0.0014642311 0.0024592 0.0002 #> T>G_ATG 0.0010868728 8.476125e-04 0.0090537776 0.0062955 0.0015 #> T>G_ATT 0.0000000000 1.075455e-03 0.0070309764 0.0095416 0.0002 #> T>G_CTA 0.0011203565 0.000000e+00 0.0019741811 0.0046233 0.0000 #> T>G_CTC 0.0010645836 2.185437e-03 0.0058242955 0.0060004 0.0013 #> T>G_CTG 0.0041885681 1.139097e-04 0.0104646545 0.0073775 0.0046 #> T>G_CTT 0.0016294096 2.533718e-03 0.0087243873 0.0091481 0.0012 #> T>G_GTA 0.0000000000 0.000000e+00 0.0041444880 0.0032461 0.0000 #> T>G_GTC 0.0000000000 1.073632e-03 0.0045019853 0.0018690 0.0000 #> T>G_GTG 0.0018775892 2.924697e-03 0.0163914526 0.0033445 0.0018 #> T>G_GTT 0.0000000000 8.250983e-04 0.0070672366 0.0056069 0.0002 #> T>G_TTA 0.0016516988 0.000000e+00 0.0054271842 0.0086563 0.0000 #> T>G_TTC 0.0000000000 0.000000e+00 0.0061602504 0.0043282 0.0003 #> T>G_TTG 0.0025727520 1.360505e-03 0.0110765263 0.0082628 0.0030 #> T>G_TTT 0.0000000000 6.951578e-05 0.0130009842 0.0000000 0.0011 #> Signature6 Signature7 #> C>A_ACA 0.0017 0.0004 #> C>A_ACC 0.0028 0.0005 #> C>A_ACG 0.0005 0.0000 #> C>A_ACT 0.0019 0.0004 #> C>A_CCA 0.0101 0.0012 #> C>A_CCC 0.0241 0.0006 #> C>A_CCG 0.0091 0.0000 #> C>A_CCT 0.0571 0.0013 #> C>A_GCA 0.0024 0.0003 #> C>A_GCC 0.0058 0.0001 #> C>A_GCG 0.0021 0.0000 #> C>A_GCT 0.0087 0.0001 #> C>A_TCA 0.0017 0.0010 #> C>A_TCC 0.0029 0.0020 #> C>A_TCG 0.0011 0.0002 #> C>A_TCT 0.0058 0.0013 #> C>G_ACA 0.0013 0.0000 #> C>G_ACC 0.0012 0.0000 #> C>G_ACG 0.0000 0.0000 #> C>G_ACT 0.0018 0.0001 #> C>G_CCA 0.0000 0.0001 #> C>G_CCC 0.0000 0.0004 #> C>G_CCG 0.0000 0.0006 #> C>G_CCT 0.0002 0.0003 #> C>G_GCA 0.0000 0.0000 #> C>G_GCC 0.0030 0.0004 #> C>G_GCG 0.0000 0.0000 #> C>G_GCT 0.0017 0.0000 #> C>G_TCA 0.0000 0.0002 #> C>G_TCC 0.0002 0.0010 #> C>G_TCG 0.0000 0.0003 #> C>G_TCT 0.0001 0.0007 #> C>T_ACA 0.0312 0.0000 #> C>T_ACC 0.0163 0.0197 #> C>T_ACG 0.0908 0.0001 #> C>T_ACT 0.0149 0.0043 #> C>T_CCA 0.0085 0.0754 #> C>T_CCC 0.0099 0.1007 #> C>T_CCG 0.0901 0.0208 #> C>T_CCT 0.0087 0.0788 #> C>T_GCA 0.0653 0.0000 #> C>T_GCC 0.0773 0.0210 #> C>T_GCG 0.1339 0.0002 #> C>T_GCT 0.0524 0.0161 #> C>T_TCA 0.0074 0.1202 #> C>T_TCC 0.0067 0.2887 #> C>T_TCG 0.0391 0.0992 #> C>T_TCT 0.0047 0.0844 #> T>A_ATA 0.0006 0.0010 #> T>A_ATC 0.0033 0.0008 #> T>A_ATG 0.0000 0.0009 #> T>A_ATT 0.0053 0.0035 #> T>A_CTA 0.0001 0.0000 #> T>A_CTC 0.0026 0.0014 #> T>A_CTG 0.0008 0.0007 #> T>A_CTT 0.0011 0.0018 #> T>A_GTA 0.0000 0.0000 #> T>A_GTC 0.0028 0.0000 #> T>A_GTG 0.0006 0.0006 #> T>A_GTT 0.0021 0.0010 #> T>A_TTA 0.0002 0.0010 #> T>A_TTC 0.0008 0.0015 #> T>A_TTG 0.0000 0.0010 #> T>A_TTT 0.0007 0.0050 #> T>C_ATA 0.0075 0.0005 #> T>C_ATC 0.0056 0.0001 #> T>C_ATG 0.0217 0.0007 #> T>C_ATT 0.0023 0.0011 #> T>C_CTA 0.0062 0.0010 #> T>C_CTC 0.0040 0.0008 #> T>C_CTG 0.0270 0.0010 #> T>C_CTT 0.0033 0.0045 #> T>C_GTA 0.0122 0.0002 #> T>C_GTC 0.0059 0.0001 #> T>C_GTG 0.0115 0.0003 #> T>C_GTT 0.0042 0.0081 #> T>C_TTA 0.0059 0.0023 #> T>C_TTC 0.0035 0.0018 #> T>C_TTG 0.0106 0.0019 #> T>C_TTT 0.0029 0.0024 #> T>G_ATA 0.0000 0.0000 #> T>G_ATC 0.0017 0.0000 #> T>G_ATG 0.0007 0.0009 #> T>G_ATT 0.0029 0.0000 #> T>G_CTA 0.0001 0.0000 #> T>G_CTC 0.0040 0.0008 #> T>G_CTG 0.0050 0.0009 #> T>G_CTT 0.0086 0.0013 #> T>G_GTA 0.0000 0.0000 #> T>G_GTC 0.0016 0.0000 #> T>G_GTG 0.0010 0.0017 #> T>G_GTT 0.0035 0.0009 #> T>G_TTA 0.0009 0.0000 #> T>G_TTC 0.0019 0.0010 #> T>G_TTG 0.0011 0.0010 #> T>G_TTT 0.0072 0.0014 #> #> Slot "exposures": #> TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08 #> Signature1 32.152658 38.32270 #> Signature13 8.682772 50.63988 #> Signature18 12.082592 6.29390 #> Signature20 16.234629 15.43989 #> Signature21 0.000000 0.00000 #> Signature22 0.000000 0.00000 #> Signature24 9.536237 5.92637 #> Signature3 22.079051 34.69719 #> Signature30 21.289529 27.48385 #> Signature4 50.583785 65.01330 #> Signature6 8.137026 12.14373 #> Signature7 11.221722 18.03919 #> TCGA-94-7557-01A-11D-2122-08 TCGA-97-7938-01A-11D-2167-08 #> Signature1 19.219138 8.482122 #> Signature13 30.013888 13.541006 #> Signature18 3.325813 10.951363 #> Signature20 9.631490 7.405128 #> Signature21 0.000000 0.000000 #> Signature22 0.000000 0.000000 #> Signature24 1.710329 7.437439 #> Signature3 9.800487 8.821790 #> Signature30 9.006214 7.117174 #> Signature4 13.468902 44.130037 #> Signature6 6.467568 2.856502 #> Signature7 14.356172 6.257438 #> TCGA-EE-A3J5-06A-11D-A20D-08 TCGA-ER-A197-06A-32D-A197-08 #> Signature1 3.731967 1.579759 #> Signature13 0.000000 0.000000 #> Signature18 0.000000 0.000000 #> Signature20 0.000000 0.000000 #> Signature21 8.099765 4.005298 #> Signature22 5.255852 1.999809 #> Signature24 0.000000 0.000000 #> Signature3 0.000000 0.000000 #> Signature30 0.000000 0.000000 #> Signature4 0.000000 0.000000 #> Signature6 0.000000 0.000000 #> Signature7 104.912416 3.415135 #> TCGA-ER-A19O-06A-11D-A197-08 #> Signature1 5.017192 #> Signature13 0.000000 #> Signature18 0.000000 #> Signature20 0.000000 #> Signature21 2.344125 #> Signature22 1.181250 #> Signature24 0.000000 #> Signature3 0.000000 #> Signature30 0.000000 #> Signature4 0.000000 #> Signature6 0.000000 #> Signature7 42.457433 #> #> Slot "table_name": #> [1] "SBS96" #> #> Slot "algorithm": #> character(0) #> #> 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_TCA #> 2 C>A_ACT #> 3 T>C_ATT #> 4 C>G_TCT #> 5 T>G_CTC #> 6 C>G_CCC #> 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> #> auto_predict_grid(musica_annot, "SBS96", cosmic_v2_sigs, "lda") #> An object of class "musica_result" #> Slot "signatures": #> Signature1 Signature3 Signature4 Signature6 Signature7 Signature13 #> C>A_ACA 1.109833e-02 0.0221723068 0.0365 0.0017 0.0004 3.347572e-04 #> C>A_ACC 9.149341e-03 0.0178716754 0.0309 0.0028 0.0005 6.487361e-04 #> C>A_ACG 1.490070e-03 0.0021383396 0.0183 0.0005 0.0000 3.814459e-05 #> C>A_ACT 6.233885e-03 0.0162651456 0.0243 0.0019 0.0004 8.466585e-04 #> C>A_CCA 6.595870e-03 0.0187817256 0.0461 0.0101 0.0012 1.710090e-03 #> C>A_CCC 7.342368e-03 0.0157604578 0.0614 0.0241 0.0006 1.159257e-03 #> C>A_CCG 8.928404e-04 0.0019633898 0.0088 0.0091 0.0000 2.441665e-04 #> C>A_CCT 7.186582e-03 0.0147228611 0.0432 0.0571 0.0013 1.256768e-03 #> C>A_GCA 8.232604e-03 0.0096965397 0.0376 0.0024 0.0003 1.321096e-04 #> C>A_GCC 5.758021e-03 0.0108433411 0.0399 0.0058 0.0001 7.542440e-04 #> C>A_GCG 6.163352e-04 0.0009291405 0.0227 0.0021 0.0000 9.682078e-05 #> C>A_GCT 4.459080e-03 0.0122153826 0.0258 0.0087 0.0001 5.511037e-04 #> C>A_TCA 1.225006e-02 0.0116532249 0.0330 0.0017 0.0010 4.816605e-02 #> C>A_TCC 1.116223e-02 0.0166067750 0.0538 0.0029 0.0020 1.732956e-02 #> C>A_TCG 2.275496e-03 0.0013572394 0.0104 0.0011 0.0002 2.293157e-03 #> C>A_TCT 1.525910e-02 0.0163280760 0.0370 0.0058 0.0013 1.863458e-02 #> C>G_ACA 1.801068e-03 0.0240026152 0.0097 0.0013 0.0000 3.775165e-03 #> C>G_ACC 2.580909e-03 0.0121603037 0.0054 0.0012 0.0000 9.208248e-04 #> C>G_ACG 5.925480e-04 0.0052754195 0.0031 0.0000 0.0000 1.989049e-05 #> C>G_ACT 2.963986e-03 0.0232776563 0.0054 0.0018 0.0001 3.860632e-03 #> C>G_CCA 1.284983e-03 0.0168325720 0.0105 0.0000 0.0001 5.333651e-03 #> C>G_CCC 7.021348e-04 0.0135314415 0.0097 0.0000 0.0004 9.123035e-04 #> C>G_CCG 5.062896e-04 0.0041764575 0.0063 0.0000 0.0006 2.854673e-04 #> C>G_CCT 1.381543e-03 0.0240463904 0.0094 0.0002 0.0003 6.383098e-03 #> C>G_GCA 6.021227e-04 0.0119168446 0.0070 0.0000 0.0000 1.349420e-03 #> C>G_GCC 2.393352e-03 0.0098236534 0.0091 0.0030 0.0004 7.888077e-04 #> C>G_GCG 2.485340e-07 0.0016710543 0.0062 0.0000 0.0000 8.179121e-05 #> C>G_GCT 8.900807e-04 0.0179143343 0.0060 0.0017 0.0000 2.680123e-03 #> C>G_TCA 1.874853e-03 0.0160414054 0.0032 0.0000 0.0002 2.802349e-01 #> C>G_TCC 2.067419e-03 0.0201499204 0.0105 0.0002 0.0010 6.388529e-02 #> C>G_TCG 3.048970e-04 0.0025279109 0.0031 0.0000 0.0003 9.528486e-03 #> C>G_TCT 3.151574e-03 0.0326736408 0.0050 0.0001 0.0007 3.302255e-01 #> C>T_ACA 2.951453e-02 0.0178721707 0.0120 0.0312 0.0000 1.480181e-03 #> C>T_ACC 1.432275e-02 0.0088960343 0.0075 0.0163 0.0197 4.050871e-05 #> C>T_ACG 1.716469e-01 0.0035727083 0.0028 0.0908 0.0001 3.165947e-04 #> C>T_ACT 1.262376e-02 0.0147976122 0.0059 0.0149 0.0043 0.000000e+00 #> C>T_CCA 2.089645e-02 0.0143950595 0.0210 0.0085 0.0754 3.647278e-03 #> C>T_CCC 1.850170e-02 0.0085447812 0.0144 0.0099 0.1007 1.004229e-03 #> C>T_CCG 9.557722e-02 0.0035184658 0.0076 0.0901 0.0208 1.292021e-04 #> C>T_CCT 1.711331e-02 0.0160755457 0.0201 0.0087 0.0788 6.117700e-04 #> C>T_GCA 2.494381e-02 0.0161272733 0.0087 0.0653 0.0000 2.934138e-03 #> C>T_GCC 2.716149e-02 0.0082086324 0.0080 0.0773 0.0210 2.515171e-03 #> C>T_GCG 1.035708e-01 0.0012129229 0.0023 0.1339 0.0002 3.205265e-03 #> C>T_GCT 1.768985e-02 0.0106116492 0.0082 0.0524 0.0161 1.687731e-03 #> C>T_TCA 1.449210e-02 0.0088802091 0.0035 0.0074 0.1202 1.138421e-01 #> C>T_TCC 1.768078e-02 0.0135295728 0.0070 0.0067 0.2887 1.502484e-02 #> C>T_TCG 7.600222e-02 0.0017054089 0.0011 0.0391 0.0992 6.102098e-03 #> C>T_TCT 1.376170e-02 0.0103044169 0.0077 0.0047 0.0844 2.814066e-02 #> T>A_ATA 4.021520e-03 0.0084285636 0.0048 0.0006 0.0010 1.243618e-03 #> T>A_ATC 2.371144e-03 0.0073730967 0.0039 0.0033 0.0008 1.060002e-03 #> T>A_ATG 2.810910e-03 0.0073573000 0.0100 0.0000 0.0009 1.025544e-04 #> T>A_ATT 8.360909e-03 0.0087539390 0.0030 0.0053 0.0035 9.718121e-04 #> T>A_CTA 1.182587e-03 0.0075713203 0.0075 0.0001 0.0000 2.851590e-04 #> T>A_CTC 1.903167e-03 0.0127254635 0.0111 0.0026 0.0014 2.222873e-04 #> T>A_CTG 1.487961e-03 0.0115085619 0.0342 0.0008 0.0007 2.869518e-04 #> T>A_CTT 2.179344e-03 0.0164561777 0.0115 0.0011 0.0018 8.004460e-07 #> T>A_GTA 6.892894e-04 0.0044347826 0.0069 0.0000 0.0000 1.379604e-04 #> T>A_GTC 5.524095e-04 0.0056154324 0.0052 0.0028 0.0000 2.528674e-04 #> T>A_GTG 1.200229e-03 0.0080701365 0.0133 0.0006 0.0006 1.535175e-04 #> T>A_GTT 2.107137e-03 0.0086791217 0.0045 0.0021 0.0010 1.227456e-04 #> T>A_TTA 5.600155e-03 0.0071326814 0.0045 0.0002 0.0010 4.032613e-04 #> T>A_TTC 1.999079e-03 0.0091027978 0.0046 0.0008 0.0015 7.718133e-04 #> T>A_TTG 1.090066e-03 0.0065658630 0.0082 0.0000 0.0010 2.451942e-04 #> T>A_TTT 3.981023e-03 0.0147121354 0.0045 0.0007 0.0050 1.603460e-04 #> T>C_ATA 1.391577e-02 0.0130357094 0.0084 0.0075 0.0005 5.494542e-04 #> T>C_ATC 6.274961e-03 0.0091862897 0.0020 0.0056 0.0001 1.455067e-04 #> T>C_ATG 1.013764e-02 0.0117169201 0.0081 0.0217 0.0007 2.791780e-04 #> T>C_ATT 9.256316e-03 0.0169788708 0.0036 0.0023 0.0011 2.674614e-04 #> T>C_CTA 4.176675e-03 0.0078950126 0.0052 0.0062 0.0010 4.275147e-05 #> T>C_CTC 5.252593e-03 0.0144311704 0.0026 0.0040 0.0008 4.330754e-05 #> T>C_CTG 7.013225e-03 0.0084229721 0.0100 0.0270 0.0010 5.427253e-05 #> T>C_CTT 6.713813e-03 0.0119324305 0.0054 0.0033 0.0045 7.639440e-07 #> T>C_GTA 1.124784e-02 0.0068500556 0.0061 0.0122 0.0002 1.054081e-03 #> T>C_GTC 6.999724e-03 0.0062607490 0.0016 0.0059 0.0001 5.298997e-04 #> T>C_GTG 4.977593e-03 0.0060987630 0.0042 0.0115 0.0003 6.300957e-04 #> T>C_GTT 1.066741e-02 0.0075093439 0.0024 0.0042 0.0081 6.761879e-04 #> T>C_TTA 8.073616e-03 0.0091154951 0.0028 0.0059 0.0023 7.840561e-04 #> T>C_TTC 4.857381e-03 0.0109537909 0.0016 0.0035 0.0018 1.329749e-04 #> T>C_TTG 8.325454e-03 0.0061130332 0.0036 0.0106 0.0019 3.740240e-05 #> T>C_TTT 6.257106e-03 0.0107743363 0.0022 0.0029 0.0024 1.797028e-04 #> T>G_ATA 1.587636e-03 0.0023513681 0.0000 0.0000 0.0000 3.861998e-04 #> T>G_ATC 1.784091e-03 0.0014642311 0.0002 0.0017 0.0000 1.123832e-04 #> T>G_ATG 1.385831e-03 0.0090537776 0.0015 0.0007 0.0009 3.600070e-05 #> T>G_ATT 3.158539e-03 0.0070309764 0.0002 0.0029 0.0000 1.924938e-04 #> T>G_CTA 3.026912e-04 0.0019741811 0.0000 0.0001 0.0000 1.509421e-05 #> T>G_CTC 2.098502e-03 0.0058242955 0.0013 0.0040 0.0008 1.476248e-04 #> T>G_CTG 1.599549e-03 0.0104646545 0.0046 0.0050 0.0009 4.598730e-05 #> T>G_CTT 2.758538e-03 0.0087243873 0.0012 0.0086 0.0013 4.637147e-04 #> T>G_GTA 9.904500e-05 0.0041444880 0.0000 0.0000 0.0000 1.848986e-05 #> T>G_GTC 2.023656e-04 0.0045019853 0.0000 0.0016 0.0000 9.337351e-05 #> T>G_GTG 1.188353e-03 0.0163914526 0.0018 0.0010 0.0017 1.057919e-05 #> T>G_GTT 8.007233e-04 0.0070672366 0.0002 0.0035 0.0009 5.374121e-05 #> T>G_TTA 1.397554e-03 0.0054271842 0.0000 0.0009 0.0000 5.465818e-04 #> T>G_TTC 1.291737e-03 0.0061602504 0.0003 0.0019 0.0010 2.353471e-04 #> T>G_TTG 2.031077e-03 0.0110765263 0.0030 0.0011 0.0010 4.790220e-07 #> T>G_TTT 4.030128e-03 0.0130009842 0.0011 0.0072 0.0014 6.705883e-04 #> Signature18 Signature21 Signature24 Signature30 #> C>A_ACA 5.053642e-02 0.0001 2.864599e-02 0.0000000 #> C>A_ACC 1.093982e-02 0.0007 2.021464e-02 0.0000000 #> C>A_ACG 2.288073e-03 0.0000 2.047900e-02 0.0019673 #> C>A_ACT 1.942409e-02 0.0006 2.460015e-02 0.0000000 #> C>A_CCA 8.876811e-02 0.0020 6.355928e-02 0.0000000 #> C>A_CCC 2.064139e-02 0.0014 3.375700e-02 0.0000000 #> C>A_CCG 1.717840e-02 0.0027 2.242899e-02 0.0022624 #> C>A_CCT 3.767696e-02 0.0056 2.008652e-02 0.0000000 #> C>A_GCA 1.287242e-01 0.0001 5.467645e-02 0.0088530 #> C>A_GCC 1.609288e-02 0.0038 1.099460e-01 0.0093449 #> C>A_GCG 9.271417e-03 0.0003 4.652487e-02 0.0008853 #> C>A_GCT 7.201707e-02 0.0023 5.042871e-02 0.0081645 #> C>A_TCA 6.708064e-02 0.0001 3.145126e-02 0.0000000 #> C>A_TCC 4.186901e-02 0.0005 6.253829e-02 0.0000000 #> C>A_TCG 1.516238e-02 0.0000 1.280259e-02 0.0016722 #> C>A_TCT 1.178778e-01 0.0004 3.029768e-02 0.0000000 #> C>G_ACA 1.516888e-03 0.0005 1.199304e-02 0.0000000 #> C>G_ACC 2.498785e-03 0.0008 8.425120e-03 0.0000000 #> C>G_ACG 2.614509e-03 0.0000 0.000000e+00 0.0048200 #> C>G_ACT 3.983011e-03 0.0018 3.881383e-03 0.0000000 #> C>G_CCA 4.584638e-04 0.0001 1.347682e-02 0.0000000 #> C>G_CCC 3.654228e-03 0.0000 1.610569e-02 0.0000000 #> C>G_CCG 5.405774e-03 0.0000 7.974720e-04 0.0032461 #> C>G_CCT 5.519605e-03 0.0003 1.038867e-02 0.0000000 #> C>G_GCA 9.238797e-04 0.0004 4.945061e-03 0.0073775 #> C>G_GCC 6.486479e-04 0.0042 9.369876e-03 0.0065906 #> C>G_GCG 5.428400e-04 0.0000 5.625727e-03 0.0015739 #> C>G_GCT 1.376725e-03 0.0004 3.055770e-03 0.0000000 #> C>G_TCA 1.802969e-03 0.0002 1.022086e-02 0.0000000 #> C>G_TCC 7.863007e-03 0.0003 7.578365e-03 0.0000000 #> C>G_TCG 1.513223e-03 0.0000 1.592714e-03 0.0019673 #> C>G_TCT 3.567102e-03 0.0003 6.100727e-03 0.0000000 #> C>T_ACA 3.825624e-03 0.0051 6.315518e-03 0.0651190 #> C>T_ACC 2.465214e-03 0.0062 3.844327e-03 0.0543970 #> C>T_ACG 8.463957e-03 0.0256 3.110664e-03 0.0204604 #> C>T_ACT 5.605740e-03 0.0030 3.420419e-03 0.0219359 #> C>T_CCA 9.767511e-03 0.0034 6.035447e-03 0.0694472 #> C>T_CCC 5.654828e-03 0.0091 0.000000e+00 0.0638403 #> C>T_CCG 1.618322e-02 0.0318 2.924419e-03 0.0173126 #> C>T_CCT 5.153319e-03 0.0040 3.971202e-03 0.0342318 #> C>T_GCA 2.703069e-03 0.0163 2.367905e-02 0.0485934 #> C>T_GCC 4.199308e-03 0.0392 1.591920e-02 0.0494787 #> C>T_GCG 1.189736e-02 0.0019 1.264808e-02 0.0157387 #> C>T_GCT 1.913381e-03 0.0166 1.812978e-02 0.0188865 #> C>T_TCA 1.492339e-02 0.0064 2.657189e-02 0.0849892 #> C>T_TCC 9.962744e-03 0.0086 1.205569e-02 0.0903010 #> C>T_TCG 1.154972e-02 0.0126 5.363360e-03 0.0151485 #> C>T_TCT 5.398014e-03 0.0064 5.532499e-03 0.0455440 #> T>A_ATA 3.037211e-03 0.0083 1.166747e-03 0.0075743 #> T>A_ATC 8.111672e-04 0.0292 1.517306e-05 0.0037380 #> T>A_ATG 4.503207e-03 0.0027 6.332456e-03 0.0065906 #> T>A_ATT 2.736523e-03 0.0043 4.967216e-06 0.0093447 #> T>A_CTA 4.123464e-04 0.0000 2.766635e-03 0.0053118 #> T>A_CTC 2.491411e-03 0.0037 2.694462e-03 0.0067873 #> T>A_CTG 5.523046e-03 0.0025 6.911165e-03 0.0082628 #> T>A_CTT 3.313713e-03 0.0010 2.915200e-03 0.0000000 #> T>A_GTA 1.875434e-03 0.0000 2.225127e-03 0.0037380 #> T>A_GTC 1.510310e-03 0.0142 4.853149e-03 0.0033445 #> T>A_GTG 1.505369e-03 0.0031 1.957586e-04 0.0050167 #> T>A_GTT 3.611025e-03 0.0041 0.000000e+00 0.0063939 #> T>A_TTA 4.663278e-03 0.0027 0.000000e+00 0.0076726 #> T>A_TTC 2.578156e-03 0.0045 7.994129e-03 0.0064922 #> T>A_TTG 2.016738e-03 0.0000 1.120214e-02 0.0036396 #> T>A_TTT 2.818679e-03 0.0008 2.705788e-04 0.0000000 #> T>C_ATA 2.933054e-03 0.0265 4.726009e-03 0.0000000 #> T>C_ATC 1.513285e-03 0.0165 6.279493e-04 0.0087547 #> T>C_ATG 3.329669e-03 0.0224 2.723759e-03 0.0090498 #> T>C_ATT 5.491318e-03 0.0189 7.122368e-03 0.0000000 #> T>C_CTA 1.921693e-04 0.0219 1.848877e-03 0.0000000 #> T>C_CTC 3.050193e-03 0.0100 4.453690e-03 0.0000000 #> T>C_CTG 2.596464e-03 0.0211 0.000000e+00 0.0000000 #> T>C_CTT 1.310029e-03 0.0204 1.597389e-03 0.0000000 #> T>C_GTA 5.291265e-04 0.1426 1.269750e-03 0.0000000 #> T>C_GTC 2.279131e-03 0.0665 6.710340e-03 0.0065906 #> T>C_GTG 5.871057e-03 0.0884 2.776850e-04 0.0078694 #> T>C_GTT 4.771566e-03 0.1003 4.238478e-03 0.0084596 #> T>C_TTA 3.023036e-04 0.0389 1.682291e-03 0.0000000 #> T>C_TTC 6.260791e-03 0.0313 2.344528e-03 0.0091481 #> T>C_TTG 1.541265e-03 0.0249 4.812742e-04 0.0060004 #> T>C_TTT 1.357797e-03 0.0274 3.581480e-04 0.0000000 #> T>G_ATA 3.861382e-04 0.0000 0.000000e+00 0.0053118 #> T>G_ATC 1.254982e-03 0.0031 1.463951e-03 0.0024592 #> T>G_ATG 2.369216e-03 0.0016 8.476125e-04 0.0062955 #> T>G_ATT 3.386029e-04 0.0018 1.075455e-03 0.0095416 #> T>G_CTA 6.100255e-05 0.0000 0.000000e+00 0.0046233 #> T>G_CTC 2.015697e-03 0.0005 2.185437e-03 0.0060004 #> T>G_CTG 5.311967e-03 0.0004 1.139097e-04 0.0073775 #> T>G_CTT 2.341629e-03 0.0032 2.533718e-03 0.0091481 #> T>G_GTA 1.341532e-03 0.0000 0.000000e+00 0.0032461 #> T>G_GTC 9.204310e-07 0.0006 1.073632e-03 0.0018690 #> T>G_GTG 9.695000e-03 0.0004 2.924697e-03 0.0033445 #> T>G_GTT 2.890554e-03 0.0008 8.250983e-04 0.0056069 #> T>G_TTA 3.631840e-05 0.0000 0.000000e+00 0.0086563 #> T>G_TTC 3.233838e-03 0.0018 0.000000e+00 0.0043282 #> T>G_TTG 7.546018e-04 0.0003 1.360505e-03 0.0082628 #> T>G_TTT 2.126442e-03 0.0003 6.951578e-05 0.0000000 #> #> Slot "exposures": #> TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08 #> Signature1 38.0547117 2.951515e+01 #> Signature3 31.1381600 4.247401e+01 #> Signature4 42.4966853 7.435720e+01 #> Signature6 9.9390431 2.892621e+01 #> Signature7 9.4448542 1.904947e+01 #> Signature13 4.4926786 5.091633e+01 #> Signature18 11.8085959 1.304692e-02 #> Signature21 0.0135092 1.664935e-02 #> Signature24 16.4973150 2.333150e-08 #> Signature30 28.1144470 2.873193e+01 #> TCGA-94-7557-01A-11D-2122-08 TCGA-97-7938-01A-11D-2167-08 #> Signature1 1.670147e+01 6.070861e+00 #> Signature3 1.272421e+01 1.701443e+00 #> Signature4 6.985214e+00 6.258025e+01 #> Signature6 1.716325e+01 1.285449e+00 #> Signature7 2.003852e+01 7.257755e+00 #> Signature13 3.200873e+01 1.282879e+01 #> Signature18 1.789642e+00 1.696400e+01 #> Signature21 4.768777e+00 1.744839e-02 #> Signature24 2.208911e-08 2.619871e-08 #> Signature30 4.820187e+00 8.294011e+00 #> TCGA-EE-A3J5-06A-11D-A20D-08 TCGA-ER-A197-06A-32D-A197-08 #> Signature1 2.237774e+00 1.265206e+00 #> Signature3 6.113964e-01 3.158933e-01 #> Signature4 2.518377e+00 1.909507e+00 #> Signature6 1.196684e-01 1.763549e-01 #> Signature7 1.002094e+02 1.567182e+00 #> Signature13 6.100717e-03 1.776477e-03 #> Signature18 1.634477e-02 1.124801e-02 #> Signature21 6.838518e+00 3.538011e+00 #> Signature24 1.552313e-08 1.810983e-08 #> Signature30 9.442458e+00 2.214822e+00 #> TCGA-ER-A19O-06A-11D-A197-08 #> Signature1 3.123445e+00 #> Signature3 1.389646e+00 #> Signature4 6.165408e-01 #> Signature6 3.090099e-01 #> Signature7 4.006470e+01 #> Signature13 6.701291e-03 #> Signature18 4.137506e-03 #> Signature21 1.346391e-02 #> Signature24 1.239909e-08 #> Signature30 5.472353e+00 #> #> 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_TCA #> 2 C>A_ACT #> 3 T>C_ATT #> 4 C>G_TCT #> 5 T>G_CTC #> 6 C>G_CCC #> 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> #>