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
)Input samples to predit signature weights
Name of table used for posterior prediction (e.g. SBS96)
Signatures to automatically subset from for prediction
Algorithm to use for prediction. Choose from "lda_posterior", decompTumor2Sig, and deconstructSigs
Annotation to grid across, if none given, prediction subsetting on all samples together
Threshold to consider a signature active in a sample
Threshold of samples to consider a signature active in the cohort
A sample will be considered active in the cohort if at least one sample has more than this threshold proportion
Print current annotation value being predicted on
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":
#> SBS1 SBS13 SBS18 SBS20 SBS21 SBS22
#> C>A_ACA 1.109833e-02 3.347572e-04 5.053642e-02 1.179962e-03 0.0001 0.0015040704
#> C>A_ACC 9.149341e-03 6.487361e-04 1.093982e-02 2.211505e-03 0.0007 0.0024510110
#> C>A_ACG 1.490070e-03 3.814459e-05 2.288073e-03 1.616910e-07 0.0000 0.0000000000
#> C>A_ACT 6.233885e-03 8.466585e-04 1.942409e-02 3.008010e-03 0.0006 0.0009224525
#> C>A_CCA 6.595870e-03 1.710090e-03 8.876811e-02 1.737711e-02 0.0020 0.0045496929
#> C>A_CCC 7.342368e-03 1.159257e-03 2.064139e-02 3.650246e-02 0.0014 0.0037644739
#> C>A_CCG 8.928404e-04 2.441665e-04 1.717840e-02 1.248259e-02 0.0027 0.0009001633
#> C>A_CCT 7.186582e-03 1.256768e-03 3.767696e-02 1.034012e-01 0.0056 0.0044398462
#> C>A_GCA 8.232604e-03 1.321096e-04 1.287242e-01 1.116124e-03 0.0001 0.0012983702
#> C>A_GCC 5.758021e-03 7.542440e-04 1.609288e-02 3.271429e-03 0.0038 0.0018096222
#> C>A_GCG 6.163352e-04 9.682078e-05 9.271417e-03 3.751613e-03 0.0003 0.0003338381
#> C>A_GCT 4.459080e-03 5.511037e-04 7.201707e-02 1.293719e-02 0.0023 0.0005191482
#> C>A_TCA 1.225006e-02 4.816605e-02 6.708064e-02 6.882997e-04 0.0001 0.0040516346
#> C>A_TCC 1.116223e-02 1.732956e-02 4.186901e-02 4.058229e-03 0.0005 0.0027397709
#> C>A_TCG 2.275496e-03 2.293157e-03 1.516238e-02 1.001102e-03 0.0000 0.0005131511
#> C>A_TCT 1.525910e-02 1.863458e-02 1.178778e-01 1.222910e-02 0.0004 0.0036056509
#> C>G_ACA 1.801068e-03 3.775165e-03 1.516888e-03 6.970411e-04 0.0005 0.0005276440
#> C>G_ACC 2.580909e-03 9.208248e-04 2.498785e-03 2.059310e-03 0.0008 0.0000000000
#> C>G_ACG 5.925480e-04 1.989049e-05 2.614509e-03 1.273496e-05 0.0000 0.0000000000
#> C>G_ACT 2.963986e-03 3.860632e-03 3.983011e-03 8.485871e-04 0.0018 0.0002994547
#> C>G_CCA 1.284983e-03 5.333651e-03 4.584638e-04 1.331626e-05 0.0001 0.0005820177
#> C>G_CCC 7.021348e-04 9.123035e-04 3.654228e-03 5.481447e-04 0.0000 0.0008252996
#> C>G_CCG 5.062896e-04 2.854673e-04 5.405774e-03 0.000000e+00 0.0000 0.0003821146
#> C>G_CCT 1.381543e-03 6.383098e-03 5.519605e-03 1.207306e-04 0.0003 0.0017606459
#> C>G_GCA 6.021227e-04 1.349420e-03 9.238797e-04 1.339769e-03 0.0004 0.0000000000
#> C>G_GCC 2.393352e-03 7.888077e-04 6.486479e-04 1.811151e-03 0.0042 0.0000000000
#> C>G_GCG 2.485340e-07 8.179121e-05 5.428400e-04 6.375380e-07 0.0000 0.0002146959
#> C>G_GCT 8.900807e-04 2.680123e-03 1.376725e-03 1.238264e-03 0.0004 0.0005384388
#> C>G_TCA 1.874853e-03 2.802349e-01 1.802969e-03 2.429847e-05 0.0002 0.0002254906
#> C>G_TCC 2.067419e-03 6.388529e-02 7.863007e-03 1.519986e-04 0.0003 0.0006286950
#> C>G_TCG 3.048970e-04 9.528486e-03 1.513223e-03 0.000000e+00 0.0000 0.0003958080
#> C>G_TCT 3.151574e-03 3.302255e-01 3.567102e-03 6.830600e-04 0.0003 0.0002573751
#> C>T_ACA 2.951453e-02 1.480181e-03 3.825624e-03 3.285805e-02 0.0051 0.0031133897
#> C>T_ACC 1.432275e-02 4.050871e-05 2.465214e-03 2.219605e-02 0.0062 0.0015248603
#> C>T_ACG 1.716469e-01 3.165947e-04 8.463957e-03 3.457201e-02 0.0256 0.0036256412
#> C>T_ACT 1.262376e-02 0.000000e+00 5.605740e-03 1.881956e-02 0.0030 0.0000000000
#> C>T_CCA 2.089645e-02 3.647278e-03 9.767511e-03 1.114519e-02 0.0034 0.0077313495
#> C>T_CCC 1.850170e-02 1.004229e-03 5.654828e-03 1.815275e-02 0.0091 0.0071108505
#> C>T_CCG 9.557722e-02 1.292021e-04 1.618322e-02 4.438494e-02 0.0318 0.0055020310
#> C>T_CCT 1.711331e-02 6.117700e-04 5.153319e-03 1.384714e-02 0.0040 0.0041697772
#> C>T_GCA 2.494381e-02 2.934138e-03 2.703069e-03 5.679395e-02 0.0163 0.0019153709
#> C>T_GCC 2.716149e-02 2.515171e-03 4.199308e-03 5.442986e-02 0.0392 0.0032291335
#> C>T_GCG 1.035708e-01 3.205265e-03 1.189736e-02 4.592689e-03 0.0019 0.0033005989
#> C>T_GCT 1.768985e-02 1.687731e-03 1.913381e-03 4.958086e-02 0.0166 0.0011140596
#> C>T_TCA 1.449210e-02 1.138421e-01 1.492339e-02 1.071032e-02 0.0064 0.0020167217
#> C>T_TCC 1.768078e-02 1.502484e-02 9.962744e-03 8.175510e-03 0.0086 0.0019908342
#> C>T_TCG 7.600222e-02 6.102098e-03 1.154972e-02 2.316390e-02 0.0126 0.0014984731
#> C>T_TCT 1.376170e-02 2.814066e-02 5.398014e-03 9.540087e-03 0.0064 0.0011822265
#> T>A_ATA 4.021520e-03 1.243618e-03 3.037211e-03 5.744014e-04 0.0083 0.0496192297
#> T>A_ATC 2.371144e-03 1.060002e-03 8.111672e-04 1.971462e-03 0.0292 0.0116667405
#> T>A_ATG 2.810910e-03 1.025544e-04 4.503207e-03 1.905866e-04 0.0027 0.0679154542
#> T>A_ATT 8.360909e-03 9.718121e-04 2.736523e-03 7.421104e-03 0.0043 0.0145999176
#> T>A_CTA 1.182587e-03 2.851590e-04 4.123464e-04 4.504236e-05 0.0000 0.0868985455
#> T>A_CTC 1.903167e-03 2.222873e-04 2.491411e-03 4.389056e-03 0.0037 0.0537068468
#> T>A_CTG 1.487961e-03 2.869518e-04 5.523046e-03 1.127836e-03 0.0025 0.2132208666
#> T>A_CTT 2.179344e-03 8.004460e-07 3.313713e-03 2.385541e-03 0.0010 0.0618275075
#> T>A_GTA 6.892894e-04 1.379604e-04 1.875434e-03 1.631298e-04 0.0000 0.0537091457
#> T>A_GTC 5.524095e-04 2.528674e-04 1.510310e-03 3.799180e-03 0.0142 0.0094893967
#> T>A_GTG 1.200229e-03 1.535175e-04 1.505369e-03 8.283337e-04 0.0031 0.0502939024
#> T>A_GTT 2.107137e-03 1.227456e-04 3.611025e-03 1.900747e-03 0.0041 0.0106014572
#> T>A_TTA 5.600155e-03 4.032613e-04 4.663278e-03 9.245480e-04 0.0027 0.0408105028
#> T>A_TTC 1.999079e-03 7.718133e-04 2.578156e-03 7.082068e-04 0.0045 0.0255703958
#> T>A_TTG 1.090066e-03 2.451942e-04 2.016738e-03 9.700313e-05 0.0000 0.0698452181
#> T>A_TTT 3.981023e-03 1.603460e-04 2.818679e-03 2.313489e-03 0.0008 0.0235790618
#> T>C_ATA 1.391577e-02 5.494542e-04 2.933054e-03 1.639506e-02 0.0265 0.0168399309
#> T>C_ATC 6.274961e-03 1.455067e-04 1.513285e-03 1.925179e-02 0.0165 0.0011082624
#> T>C_ATG 1.013764e-02 2.791780e-04 3.329669e-03 5.478492e-02 0.0224 0.0049136164
#> T>C_ATT 9.256316e-03 2.674614e-04 5.491318e-03 7.341270e-03 0.0189 0.0026305239
#> T>C_CTA 4.176675e-03 4.275147e-05 1.921693e-04 1.486770e-02 0.0219 0.0040273463
#> T>C_CTC 5.252593e-03 4.330754e-05 3.050193e-03 1.835616e-02 0.0100 0.0013524439
#> T>C_CTG 7.013225e-03 5.427253e-05 2.596464e-03 7.415056e-02 0.0211 0.0027496661
#> T>C_CTT 6.713813e-03 7.639440e-07 1.310029e-03 1.100112e-02 0.0204 0.0023633535
#> T>C_GTA 1.124784e-02 1.054081e-03 5.291265e-04 2.469317e-03 0.1426 0.0042174541
#> T>C_GTC 6.999724e-03 5.298997e-04 2.279131e-03 1.565633e-03 0.0665 0.0000000000
#> T>C_GTG 4.977593e-03 6.300957e-04 5.871057e-03 2.734176e-02 0.0884 0.0014748845
#> T>C_GTT 1.066741e-02 6.761879e-04 4.771566e-03 1.498265e-03 0.1003 0.0015610427
#> T>C_TTA 8.073616e-03 7.840561e-04 3.023036e-04 5.734230e-03 0.0389 0.0048036697
#> T>C_TTC 4.857381e-03 1.329749e-04 6.260791e-03 1.123425e-02 0.0313 0.0009121575
#> T>C_TTG 8.325454e-03 3.740240e-05 1.541265e-03 2.376761e-02 0.0249 0.0017817357
#> T>C_TTT 6.257106e-03 1.797028e-04 1.357797e-03 5.395186e-03 0.0274 0.0000000000
#> T>G_ATA 1.587636e-03 3.861998e-04 3.861382e-04 1.765291e-06 0.0000 0.0016519986
#> T>G_ATC 1.784091e-03 1.123832e-04 1.254982e-03 3.813879e-04 0.0031 0.0000000000
#> T>G_ATG 1.385831e-03 3.600070e-05 2.369216e-03 6.587581e-04 0.0016 0.0010868728
#> T>G_ATT 3.158539e-03 1.924938e-04 3.386029e-04 5.321252e-04 0.0018 0.0000000000
#> T>G_CTA 3.026912e-04 1.509421e-05 6.100255e-05 2.326408e-05 0.0000 0.0011203565
#> T>G_CTC 2.098502e-03 1.476248e-04 2.015697e-03 8.476495e-03 0.0005 0.0010645836
#> T>G_CTG 1.599549e-03 4.598730e-05 5.311967e-03 1.538378e-02 0.0004 0.0041885681
#> T>G_CTT 2.758538e-03 4.637147e-04 2.341629e-03 2.185395e-03 0.0032 0.0016294096
#> T>G_GTA 9.904500e-05 1.848986e-05 1.341532e-03 3.579149e-06 0.0000 0.0000000000
#> T>G_GTC 2.023656e-04 9.337351e-05 9.204310e-07 2.830575e-03 0.0006 0.0000000000
#> T>G_GTG 1.188353e-03 1.057919e-05 9.695000e-03 2.733219e-03 0.0004 0.0018775892
#> T>G_GTT 8.007233e-04 5.374121e-05 2.890554e-03 3.558559e-03 0.0008 0.0000000000
#> T>G_TTA 1.397554e-03 5.465818e-04 3.631840e-05 2.691470e-07 0.0000 0.0016516988
#> T>G_TTC 1.291737e-03 2.353471e-04 3.233838e-03 3.772344e-04 0.0018 0.0000000000
#> T>G_TTG 2.031077e-03 4.790220e-07 7.546018e-04 5.154216e-04 0.0003 0.0025727520
#> T>G_TTT 4.030128e-03 6.705883e-04 2.126442e-03 6.156567e-04 0.0003 0.0000000000
#> SBS24 SBS3 SBS30 SBS4 SBS6 SBS7
#> C>A_ACA 2.864599e-02 0.0221723068 0.0000000 0.0365 0.0017 0.0004
#> C>A_ACC 2.021464e-02 0.0178716754 0.0000000 0.0309 0.0028 0.0005
#> C>A_ACG 2.047900e-02 0.0021383396 0.0019673 0.0183 0.0005 0.0000
#> C>A_ACT 2.460015e-02 0.0162651456 0.0000000 0.0243 0.0019 0.0004
#> C>A_CCA 6.355928e-02 0.0187817256 0.0000000 0.0461 0.0101 0.0012
#> C>A_CCC 3.375700e-02 0.0157604578 0.0000000 0.0614 0.0241 0.0006
#> C>A_CCG 2.242899e-02 0.0019633898 0.0022624 0.0088 0.0091 0.0000
#> C>A_CCT 2.008652e-02 0.0147228611 0.0000000 0.0432 0.0571 0.0013
#> C>A_GCA 5.467645e-02 0.0096965397 0.0088530 0.0376 0.0024 0.0003
#> C>A_GCC 1.099460e-01 0.0108433411 0.0093449 0.0399 0.0058 0.0001
#> C>A_GCG 4.652487e-02 0.0009291405 0.0008853 0.0227 0.0021 0.0000
#> C>A_GCT 5.042871e-02 0.0122153826 0.0081645 0.0258 0.0087 0.0001
#> C>A_TCA 3.145126e-02 0.0116532249 0.0000000 0.0330 0.0017 0.0010
#> C>A_TCC 6.253829e-02 0.0166067750 0.0000000 0.0538 0.0029 0.0020
#> C>A_TCG 1.280259e-02 0.0013572394 0.0016722 0.0104 0.0011 0.0002
#> C>A_TCT 3.029768e-02 0.0163280760 0.0000000 0.0370 0.0058 0.0013
#> C>G_ACA 1.199304e-02 0.0240026152 0.0000000 0.0097 0.0013 0.0000
#> C>G_ACC 8.425120e-03 0.0121603037 0.0000000 0.0054 0.0012 0.0000
#> C>G_ACG 0.000000e+00 0.0052754195 0.0048200 0.0031 0.0000 0.0000
#> C>G_ACT 3.881383e-03 0.0232776563 0.0000000 0.0054 0.0018 0.0001
#> C>G_CCA 1.347682e-02 0.0168325720 0.0000000 0.0105 0.0000 0.0001
#> C>G_CCC 1.610569e-02 0.0135314415 0.0000000 0.0097 0.0000 0.0004
#> C>G_CCG 7.974720e-04 0.0041764575 0.0032461 0.0063 0.0000 0.0006
#> C>G_CCT 1.038867e-02 0.0240463904 0.0000000 0.0094 0.0002 0.0003
#> C>G_GCA 4.945061e-03 0.0119168446 0.0073775 0.0070 0.0000 0.0000
#> C>G_GCC 9.369876e-03 0.0098236534 0.0065906 0.0091 0.0030 0.0004
#> C>G_GCG 5.625727e-03 0.0016710543 0.0015739 0.0062 0.0000 0.0000
#> C>G_GCT 3.055770e-03 0.0179143343 0.0000000 0.0060 0.0017 0.0000
#> C>G_TCA 1.022086e-02 0.0160414054 0.0000000 0.0032 0.0000 0.0002
#> C>G_TCC 7.578365e-03 0.0201499204 0.0000000 0.0105 0.0002 0.0010
#> C>G_TCG 1.592714e-03 0.0025279109 0.0019673 0.0031 0.0000 0.0003
#> C>G_TCT 6.100727e-03 0.0326736408 0.0000000 0.0050 0.0001 0.0007
#> C>T_ACA 6.315518e-03 0.0178721707 0.0651190 0.0120 0.0312 0.0000
#> C>T_ACC 3.844327e-03 0.0088960343 0.0543970 0.0075 0.0163 0.0197
#> C>T_ACG 3.110664e-03 0.0035727083 0.0204604 0.0028 0.0908 0.0001
#> C>T_ACT 3.420419e-03 0.0147976122 0.0219359 0.0059 0.0149 0.0043
#> C>T_CCA 6.035447e-03 0.0143950595 0.0694472 0.0210 0.0085 0.0754
#> C>T_CCC 0.000000e+00 0.0085447812 0.0638403 0.0144 0.0099 0.1007
#> C>T_CCG 2.924419e-03 0.0035184658 0.0173126 0.0076 0.0901 0.0208
#> C>T_CCT 3.971202e-03 0.0160755457 0.0342318 0.0201 0.0087 0.0788
#> C>T_GCA 2.367905e-02 0.0161272733 0.0485934 0.0087 0.0653 0.0000
#> C>T_GCC 1.591920e-02 0.0082086324 0.0494787 0.0080 0.0773 0.0210
#> C>T_GCG 1.264808e-02 0.0012129229 0.0157387 0.0023 0.1339 0.0002
#> C>T_GCT 1.812978e-02 0.0106116492 0.0188865 0.0082 0.0524 0.0161
#> C>T_TCA 2.657189e-02 0.0088802091 0.0849892 0.0035 0.0074 0.1202
#> C>T_TCC 1.205569e-02 0.0135295728 0.0903010 0.0070 0.0067 0.2887
#> C>T_TCG 5.363360e-03 0.0017054089 0.0151485 0.0011 0.0391 0.0992
#> C>T_TCT 5.532499e-03 0.0103044169 0.0455440 0.0077 0.0047 0.0844
#> T>A_ATA 1.166747e-03 0.0084285636 0.0075743 0.0048 0.0006 0.0010
#> T>A_ATC 1.517306e-05 0.0073730967 0.0037380 0.0039 0.0033 0.0008
#> T>A_ATG 6.332456e-03 0.0073573000 0.0065906 0.0100 0.0000 0.0009
#> T>A_ATT 4.967216e-06 0.0087539390 0.0093447 0.0030 0.0053 0.0035
#> T>A_CTA 2.766635e-03 0.0075713203 0.0053118 0.0075 0.0001 0.0000
#> T>A_CTC 2.694462e-03 0.0127254635 0.0067873 0.0111 0.0026 0.0014
#> T>A_CTG 6.911165e-03 0.0115085619 0.0082628 0.0342 0.0008 0.0007
#> T>A_CTT 2.915200e-03 0.0164561777 0.0000000 0.0115 0.0011 0.0018
#> T>A_GTA 2.225127e-03 0.0044347826 0.0037380 0.0069 0.0000 0.0000
#> T>A_GTC 4.853149e-03 0.0056154324 0.0033445 0.0052 0.0028 0.0000
#> T>A_GTG 1.957586e-04 0.0080701365 0.0050167 0.0133 0.0006 0.0006
#> T>A_GTT 0.000000e+00 0.0086791217 0.0063939 0.0045 0.0021 0.0010
#> T>A_TTA 0.000000e+00 0.0071326814 0.0076726 0.0045 0.0002 0.0010
#> T>A_TTC 7.994129e-03 0.0091027978 0.0064922 0.0046 0.0008 0.0015
#> T>A_TTG 1.120214e-02 0.0065658630 0.0036396 0.0082 0.0000 0.0010
#> T>A_TTT 2.705788e-04 0.0147121354 0.0000000 0.0045 0.0007 0.0050
#> T>C_ATA 4.726009e-03 0.0130357094 0.0000000 0.0084 0.0075 0.0005
#> T>C_ATC 6.279493e-04 0.0091862897 0.0087547 0.0020 0.0056 0.0001
#> T>C_ATG 2.723759e-03 0.0117169201 0.0090498 0.0081 0.0217 0.0007
#> T>C_ATT 7.122368e-03 0.0169788708 0.0000000 0.0036 0.0023 0.0011
#> T>C_CTA 1.848877e-03 0.0078950126 0.0000000 0.0052 0.0062 0.0010
#> T>C_CTC 4.453690e-03 0.0144311704 0.0000000 0.0026 0.0040 0.0008
#> T>C_CTG 0.000000e+00 0.0084229721 0.0000000 0.0100 0.0270 0.0010
#> T>C_CTT 1.597389e-03 0.0119324305 0.0000000 0.0054 0.0033 0.0045
#> T>C_GTA 1.269750e-03 0.0068500556 0.0000000 0.0061 0.0122 0.0002
#> T>C_GTC 6.710340e-03 0.0062607490 0.0065906 0.0016 0.0059 0.0001
#> T>C_GTG 2.776850e-04 0.0060987630 0.0078694 0.0042 0.0115 0.0003
#> T>C_GTT 4.238478e-03 0.0075093439 0.0084596 0.0024 0.0042 0.0081
#> T>C_TTA 1.682291e-03 0.0091154951 0.0000000 0.0028 0.0059 0.0023
#> T>C_TTC 2.344528e-03 0.0109537909 0.0091481 0.0016 0.0035 0.0018
#> T>C_TTG 4.812742e-04 0.0061130332 0.0060004 0.0036 0.0106 0.0019
#> T>C_TTT 3.581480e-04 0.0107743363 0.0000000 0.0022 0.0029 0.0024
#> T>G_ATA 0.000000e+00 0.0023513681 0.0053118 0.0000 0.0000 0.0000
#> T>G_ATC 1.463951e-03 0.0014642311 0.0024592 0.0002 0.0017 0.0000
#> T>G_ATG 8.476125e-04 0.0090537776 0.0062955 0.0015 0.0007 0.0009
#> T>G_ATT 1.075455e-03 0.0070309764 0.0095416 0.0002 0.0029 0.0000
#> T>G_CTA 0.000000e+00 0.0019741811 0.0046233 0.0000 0.0001 0.0000
#> T>G_CTC 2.185437e-03 0.0058242955 0.0060004 0.0013 0.0040 0.0008
#> T>G_CTG 1.139097e-04 0.0104646545 0.0073775 0.0046 0.0050 0.0009
#> T>G_CTT 2.533718e-03 0.0087243873 0.0091481 0.0012 0.0086 0.0013
#> T>G_GTA 0.000000e+00 0.0041444880 0.0032461 0.0000 0.0000 0.0000
#> T>G_GTC 1.073632e-03 0.0045019853 0.0018690 0.0000 0.0016 0.0000
#> T>G_GTG 2.924697e-03 0.0163914526 0.0033445 0.0018 0.0010 0.0017
#> T>G_GTT 8.250983e-04 0.0070672366 0.0056069 0.0002 0.0035 0.0009
#> T>G_TTA 0.000000e+00 0.0054271842 0.0086563 0.0000 0.0009 0.0000
#> T>G_TTC 0.000000e+00 0.0061602504 0.0043282 0.0003 0.0019 0.0010
#> T>G_TTG 1.360505e-03 0.0110765263 0.0082628 0.0030 0.0011 0.0010
#> T>G_TTT 6.951578e-05 0.0130009842 0.0000000 0.0011 0.0072 0.0014
#>
#> Slot "exposures":
#> TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08
#> SBS1 32.152658 38.32270
#> SBS13 8.682772 50.63988
#> SBS18 12.082592 6.29390
#> SBS20 16.234629 15.43989
#> SBS21 0.000000 0.00000
#> SBS22 0.000000 0.00000
#> SBS24 9.536237 5.92637
#> SBS3 22.079051 34.69719
#> SBS30 21.289529 27.48385
#> SBS4 50.583785 65.01330
#> SBS6 8.137026 12.14373
#> SBS7 11.221722 18.03919
#> TCGA-94-7557-01A-11D-2122-08 TCGA-97-7938-01A-11D-2167-08
#> SBS1 19.219138 8.482122
#> SBS13 30.013888 13.541006
#> SBS18 3.325813 10.951363
#> SBS20 9.631490 7.405128
#> SBS21 0.000000 0.000000
#> SBS22 0.000000 0.000000
#> SBS24 1.710329 7.437439
#> SBS3 9.800487 8.821790
#> SBS30 9.006214 7.117174
#> SBS4 13.468902 44.130037
#> SBS6 6.467568 2.856502
#> SBS7 14.356172 6.257438
#> TCGA-EE-A3J5-06A-11D-A20D-08 TCGA-ER-A197-06A-32D-A197-08
#> SBS1 3.731967 1.579759
#> SBS13 0.000000 0.000000
#> SBS18 0.000000 0.000000
#> SBS20 0.000000 0.000000
#> SBS21 8.099765 4.005298
#> SBS22 5.255852 1.999809
#> SBS24 0.000000 0.000000
#> SBS3 0.000000 0.000000
#> SBS30 0.000000 0.000000
#> SBS4 0.000000 0.000000
#> SBS6 0.000000 0.000000
#> SBS7 104.912416 3.415135
#> TCGA-ER-A19O-06A-11D-A197-08
#> SBS1 5.017192
#> SBS13 0.000000
#> SBS18 0.000000
#> SBS20 0.000000
#> SBS21 2.344125
#> SBS22 1.181250
#> SBS24 0.000000
#> SBS3 0.000000
#> SBS30 0.000000
#> SBS4 0.000000
#> SBS6 0.000000
#> SBS7 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
#> <fctr> <num> <num> <char> <char> <fctr>
#> 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
#> <char>
#> 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
#> <fctr> <char>
#> 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":
#> SBS1 SBS3 SBS4 SBS6 SBS7 SBS13
#> 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
#> SBS18 SBS21 SBS24 SBS30
#> 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
#> SBS1 38.0547117 2.951515e+01
#> SBS3 31.1381600 4.247401e+01
#> SBS4 42.4966853 7.435720e+01
#> SBS6 9.9390431 2.892621e+01
#> SBS7 9.4448542 1.904947e+01
#> SBS13 4.4926786 5.091633e+01
#> SBS18 11.8085959 1.304692e-02
#> SBS21 0.0135092 1.664935e-02
#> SBS24 16.4973150 2.333150e-08
#> SBS30 28.1144470 2.873193e+01
#> TCGA-94-7557-01A-11D-2122-08 TCGA-97-7938-01A-11D-2167-08
#> SBS1 1.670147e+01 6.070861e+00
#> SBS3 1.272421e+01 1.701443e+00
#> SBS4 6.985214e+00 6.258025e+01
#> SBS6 1.716325e+01 1.285449e+00
#> SBS7 2.003852e+01 7.257755e+00
#> SBS13 3.200873e+01 1.282879e+01
#> SBS18 1.789642e+00 1.696400e+01
#> SBS21 4.768777e+00 1.744839e-02
#> SBS24 2.208911e-08 2.619871e-08
#> SBS30 4.820187e+00 8.294011e+00
#> TCGA-EE-A3J5-06A-11D-A20D-08 TCGA-ER-A197-06A-32D-A197-08
#> SBS1 2.237774e+00 1.265206e+00
#> SBS3 6.113964e-01 3.158933e-01
#> SBS4 2.518377e+00 1.909507e+00
#> SBS6 1.196684e-01 1.763549e-01
#> SBS7 1.002094e+02 1.567182e+00
#> SBS13 6.100717e-03 1.776477e-03
#> SBS18 1.634477e-02 1.124801e-02
#> SBS21 6.838518e+00 3.538011e+00
#> SBS24 1.552313e-08 1.810983e-08
#> SBS30 9.442458e+00 2.214822e+00
#> TCGA-ER-A19O-06A-11D-A197-08
#> SBS1 3.123445e+00
#> SBS3 1.389646e+00
#> SBS4 6.165408e-01
#> SBS6 3.090099e-01
#> SBS7 4.006470e+01
#> SBS13 6.701291e-03
#> SBS18 4.137506e-03
#> SBS21 1.346391e-02
#> SBS24 1.239909e-08
#> SBS30 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
#> <fctr> <num> <num> <char> <char> <fctr>
#> 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
#> <char>
#> 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
#> <fctr> <char>
#> 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>
#>