R/sig_auto_extract.R
sig_auto_extract.RdA bayesian variant of NMF algorithm to enable optimal inferences for the number of signatures through the automatic relevance determination technique. This functions delevers highly interpretable and sparse representations for both signature profiles and attributions at a balance between data fitting and model complexity (this method may introduce more signatures than expected, especially for copy number signatures (thus I don't recommend you to use this feature to extract copy number signatures)). See detail part and references for more.
a matrix used for NMF decomposition with rows indicate samples and columns indicate components.
prefix for result data files.
path to save data runs, default is tempdir().
default is "L1W.L2H", which uses an exponential prior for W and a half-normal prior for H (This method is used by PCAWG project, see reference #3). You can also use "L1KL" to set expoential priors for both W and H, and "L2KL" to set half-normal priors for both W and H. The latter two methods are originally implemented by SignatureAnalyzer software.
the selection strategy for returned data. Set 'stable' for getting optimal
result from the most frequent K. Set 'optimal' for getting optimal result from all Ks.
Set 'ms' for getting result with maximum mean cosine similarity with provided reference
signatures. See ref_sigs option for details.
If you want select other solution, please check get_bayesian_result.
A Signature object or matrix or string for specifying
reference signatures, only used when strategy = 'ms'.
See Signature and sig_db options in get_sig_similarity for details.
number of initial signatures.
number of independent simulations.
the maximum number of iterations.
tolerance for convergence.
number of cpu cores to run NMF.
if TRUE, then refit the denovo signatures with QP method, see sig_fit.
if TRUE, it will skip running a previous stored result. This can be used to
extend run times, e.g. you try running 10 times firstly and then you want to extend it to
20 times.
if TRUE, try to recover result from previous runs based on input result_prefix,
destdir and nrun. This is pretty useful for reproducing result. Please use skip if you want
to recover an unfinished job.
a list with Signature class.
There are three methods available in this function: "L1W.L2H", "L1KL" and "L2KL".
They use different priors for the bayesian variant of NMF algorithm
(see method parameter) written by reference #1 and implemented in
SignatureAnalyzer software
(reference #2).
I copied source code for the three methods from Broad Institute and supplementary
files of reference #3, and wrote this higher function. It is more friendly for users
to extract, visualize and analyze signatures by combining with other powerful functions
in sigminer package. Besides, I implemented parallel computation to speed up
the calculation process and a similar input and output structure like sig_extract().
Tan, Vincent YF, and Cédric Févotte. "Automatic relevance determination in nonnegative matrix factorization with the/spl beta/-divergence." IEEE Transactions on Pattern Analysis and Machine Intelligence 35.7 (2012): 1592-1605.
Kim, Jaegil, et al. "Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors." Nature genetics 48.6 (2016): 600.
Alexandrov, Ludmil, et al. "The repertoire of mutational signatures in human cancer." BioRxiv (2018): 322859.
sig_tally for getting variation matrix, sig_extract for extracting signatures using NMF package, sig_estimate for estimating signature number for sig_extract.
# \donttest{
load(system.file("extdata", "toy_copynumber_tally_W.RData",
package = "sigminer", mustWork = TRUE
))
res <- sig_auto_extract(cn_tally_W$nmf_matrix, result_prefix = "Test_copynumber", nrun = 1)
#> Select Run 1, which K = 2 as best solution.
# At default, all run files are stored in tempdir()
dir(tempdir(), pattern = "Test_copynumber")
#> [1] "Test_copynumber.1.rds"
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read_maf(maf = laml.maf)
#> -Reading
#> -Validating
#> -Silent variants: 475
#> -Summarizing
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.170s elapsed (0.211s cpu)
mt_tally <- sig_tally(
laml,
ref_genome = "BSgenome.Hsapiens.UCSC.hg19",
use_syn = TRUE
)
#> ℹ [2024-03-13 10:52:39.321204]: Started.
#> ℹ [2024-03-13 10:52:39.325443]: We would assume you marked all variants' position in + strand.
#> ✔ [2024-03-13 10:52:39.327311]: Reference genome loaded.
#> ✔ [2024-03-13 10:52:39.33178]: Variants from MAF object queried.
#> ✔ [2024-03-13 10:52:39.334143]: Chromosome names checked.
#> ✔ [2024-03-13 10:52:39.337384]: Sex chromosomes properly handled.
#> ✔ [2024-03-13 10:52:39.339015]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept.
#> ✔ [2024-03-13 10:52:39.344189]: Variant start and end position checked.
#> ✔ [2024-03-13 10:52:39.348312]: Variant data for matrix generation preprocessed.
#> ℹ [2024-03-13 10:52:39.349706]: SBS matrix generation - start.
#> ℹ [2024-03-13 10:52:39.351612]: Extracting 5' and 3' adjacent bases.
#> ℹ [2024-03-13 10:52:39.666478]: Extracting +/- 20bp around mutated bases for background C>T estimation.
#> ℹ [2024-03-13 10:52:40.014906]: Estimating APOBEC enrichment scores.
#> ℹ [2024-03-13 10:52:40.016941]: Performing one-way Fisher's test for APOBEC enrichment.
#> ✔ [2024-03-13 10:52:40.091566]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples)
#> ℹ [2024-03-13 10:52:40.095167]: Creating SBS sample-by-component matrices.
#> ✔ [2024-03-13 10:52:40.099787]: SBS-6 matrix created.
#> ✔ [2024-03-13 10:52:40.104901]: SBS-96 matrix created.
#> ✔ [2024-03-13 10:52:40.119379]: SBS-1536 matrix created.
#> ℹ [2024-03-13 10:52:40.121194]: Return SBS-96 as major matrix.
#> ✔ [2024-03-13 10:52:40.124294]: Done.
#> ℹ [2024-03-13 10:52:40.125776]: 0.805 secs elapsed.
x <- sig_auto_extract(mt_tally$nmf_matrix,
strategy = "ms", nrun = 3, ref_sigs = "legacy"
)
#> The follow samples dropped due to null catalogue:
#> TCGA-AB-2823, TCGA-AB-2840, TCGA-AB-2848, TCGA-AB-2909, TCGA-AB-2942
#> Solutions ordered by mean cosine similarity to references:
#> Run#2:K#2 Run#3:K#2 Run#1:K#3
#> 0.7180000 0.6755000 0.6113333
#> Details:
#> $`Run#1:K#3`
#> COSMIC_1 COSMIC_11 COSMIC_16
#> 0.959 0.457 0.418
#>
#> $`Run#2:K#2`
#> COSMIC_1 COSMIC_10
#> 0.911 0.525
#>
#> $`Run#3:K#2`
#> COSMIC_1 COSMIC_19
#> 0.960 0.391
#>
#> Select Run 2, which K = 2 as best solution.
x
#> $Signature
#> Sig1 Sig2
#> A[C>A]A 1.580849e+01 3.354537e-43
#> A[C>A]C 2.696742e+01 1.711302e-146
#> A[C>A]G 3.719645e+00 0.000000e+00
#> A[C>A]T 4.369948e-101 5.629483e+00
#> A[C>G]A 1.301876e+01 5.218037e-14
#> A[C>G]C 5.579467e+00 1.790773e-42
#> A[C>G]G 7.439289e+00 6.623960e-295
#> A[C>G]T 7.439289e+00 1.665300e-92
#> A[C>T]A 4.742547e+01 2.507544e-99
#> A[C>T]C 4.742547e+01 3.365275e-110
#> A[C>T]G 2.148095e+02 2.046864e-70
#> A[C>T]T 2.417769e+01 2.494609e-141
#> A[T>A]A 4.435226e-169 2.646557e-74
#> A[T>A]C 1.115893e+01 2.473039e-100
#> A[T>A]G 2.512097e-127 4.222112e+00
#> A[T>A]T 3.719645e+00 6.916129e-319
#> A[T>C]A 2.603751e+01 1.886028e-76
#> A[T>C]C 1.115893e+01 9.907872e-10
#> A[T>C]G 2.510759e+01 6.336350e-06
#> A[T>C]T 2.882725e+01 2.323630e-22
#> A[T>G]A 5.579467e+00 1.370245e-53
#> A[T>G]C 0.000000e+00 1.407371e+00
#> A[T>G]G 2.789733e+00 9.268124e-134
#> A[T>G]T 2.789733e+00 1.507417e-242
#> C[C>A]A 1.673840e+01 0.000000e+00
#> C[C>A]C 3.781832e-122 1.055528e+01
#> C[C>A]G 1.301876e+01 5.710966e-238
#> C[C>A]T 1.673840e+01 2.687738e-70
#> C[C>G]A 1.208884e+01 7.292559e-15
#> C[C>G]C 3.719645e+00 0.000000e+00
#> C[C>G]G 1.394862e+01 3.939853e-05
#> C[C>G]T 6.509378e+00 1.243146e-20
#> C[C>T]A 3.812636e+01 7.525394e-244
#> C[C>T]C 2.789733e+01 3.656930e-123
#> C[C>T]G 1.850063e+02 4.256959e+00
#> C[C>T]T 5.579467e+01 1.355036e-88
#> C[T>A]A 5.343519e-104 1.152078e-88
#> C[T>A]C 4.471475e+00 3.653185e+00
#> C[T>A]G 1.115893e+01 3.531131e-108
#> C[T>A]T 4.649556e+00 0.000000e+00
#> C[T>C]A 2.283856e-36 4.925797e+00
#> C[T>C]C 1.673840e+01 2.607810e-110
#> C[T>C]G 1.157591e-150 1.337002e+01
#> C[T>C]T 1.394867e+01 2.381950e-36
#> C[T>G]A 9.299111e-01 0.000000e+00
#> C[T>G]C 4.128422e-101 5.629483e+00
#> C[T>G]G 9.299111e+00 0.000000e+00
#> C[T>G]T 4.649556e+00 1.981648e-149
#> G[C>A]A 1.191639e+01 2.945243e+00
#> G[C>A]C 8.369200e+00 6.440726e-203
#> G[C>A]G 4.649556e+00 0.000000e+00
#> G[C>A]T 4.759607e-164 6.333168e+00
#> G[C>G]A 1.022902e+01 1.431919e-204
#> G[C>G]C 6.509378e+00 7.469539e-147
#> G[C>G]G 6.509378e+00 0.000000e+00
#> G[C>G]T 1.906852e-13 4.222112e+00
#> G[C>T]A 1.629196e-100 1.899950e+01
#> G[C>T]C 4.556565e+01 4.293728e-92
#> G[C>T]G 1.716289e+02 3.120988e+00
#> G[C>T]T 4.742547e+01 6.360692e-34
#> G[T>A]A 4.011672e-306 1.407371e+00
#> G[T>A]C 5.721564e-171 6.333168e+00
#> G[T>A]G 3.719645e+00 1.387479e-103
#> G[T>A]T 3.265340e-25 4.222112e+00
#> G[T>C]A 5.690453e-39 4.222112e+00
#> G[T>C]C 5.647862e-148 6.333168e+00
#> G[T>C]G 1.022902e+01 3.978697e-195
#> G[T>C]T 2.777612e-129 8.444224e+00
#> G[T>G]A 4.800309e-95 2.814741e+00
#> G[T>G]C 2.789733e+00 7.173285e-226
#> G[T>G]G 5.579467e+00 7.593900e-26
#> G[T>G]T 1.859822e+00 0.000000e+00
#> T[C>A]A 4.511174e+00 5.734199e+00
#> T[C>A]C 2.138796e+01 6.320816e-116
#> T[C>A]G 7.439289e+00 5.186619e-135
#> T[C>A]T 2.603751e+01 2.240206e-180
#> T[C>G]A 4.649556e+00 7.740270e-287
#> T[C>G]C 1.032515e-31 5.629483e+00
#> T[C>G]G 1.022902e+01 1.902746e-259
#> T[C>G]T 3.475291e-185 6.333168e+00
#> T[C>T]A 3.998613e+01 3.426904e-05
#> T[C>T]C 3.998618e+01 5.934640e-151
#> T[C>T]G 2.473771e-32 7.810907e+01
#> T[C>T]T 2.510760e+01 5.659784e-27
#> T[T>A]A 0.000000e+00 7.710426e-294
#> T[T>A]C 3.719645e+00 1.628685e-111
#> T[T>A]G 0.000000e+00 2.814741e+00
#> T[T>A]T 4.649556e+00 8.122779e-107
#> T[T>C]A 0.000000e+00 1.407371e+00
#> T[T>C]C 8.369200e+00 7.358783e-268
#> T[T>C]G 9.299111e+00 0.000000e+00
#> T[T>C]T 1.859822e+01 3.315674e-136
#> T[T>G]A 2.789733e+00 0.000000e+00
#> T[T>G]C 4.649556e+00 4.438833e-146
#> T[T>G]G 1.859822e+00 0.000000e+00
#> T[T>G]T 4.649556e+00 0.000000e+00
#>
#> $Signature.norm
#> Sig1 Sig2
#> A[C>A]A 1.012514e-02 1.503766e-45
#> A[C>A]C 1.727229e-02 7.671396e-149
#> A[C>A]G 2.382386e-03 0.000000e+00
#> A[C>A]T 2.798897e-104 2.523575e-02
#> A[C>G]A 8.338349e-03 2.339132e-16
#> A[C>G]C 3.573578e-03 8.027646e-45
#> A[C>G]G 4.764771e-03 2.969377e-297
#> A[C>G]T 4.764771e-03 7.465178e-95
#> A[C>T]A 3.037542e-02 1.124078e-101
#> A[C>T]C 3.037542e-02 1.508580e-112
#> A[C>T]G 1.375828e-01 9.175645e-73
#> A[C>T]T 1.548551e-02 1.118279e-143
#> A[T>A]A 2.840706e-172 1.186394e-76
#> A[T>A]C 7.147157e-03 1.108610e-102
#> A[T>A]G 1.608966e-130 1.892681e-02
#> A[T>A]T 2.382386e-03 3.102732e-321
#> A[T>C]A 1.667670e-02 8.454653e-79
#> A[T>C]C 7.147157e-03 4.441484e-12
#> A[T>C]G 1.608110e-02 2.840448e-08
#> A[T>C]T 1.846349e-02 1.041633e-24
#> A[T>G]A 3.573578e-03 6.142513e-56
#> A[T>G]C 0.000000e+00 6.308937e-03
#> A[T>G]G 1.786789e-03 4.154699e-136
#> A[T>G]T 1.786789e-03 6.757422e-245
#> C[C>A]A 1.072073e-02 0.000000e+00
#> C[C>A]C 2.422216e-125 4.731703e-02
#> C[C>A]G 8.338349e-03 2.560102e-240
#> C[C>A]T 1.072073e-02 1.204854e-72
#> C[C>G]A 7.742753e-03 3.269096e-17
#> C[C>G]C 2.382386e-03 0.000000e+00
#> C[C>G]G 8.933912e-03 1.766151e-07
#> C[C>G]T 4.169175e-03 5.572753e-23
#> C[C>T]A 2.441945e-02 3.373471e-246
#> C[C>T]C 1.786789e-02 1.639322e-125
#> C[C>T]G 1.184942e-01 1.908302e-02
#> C[C>T]T 3.573578e-02 6.074330e-91
#> C[T>A]A 3.422457e-107 5.164515e-91
#> C[T>A]C 2.863923e-03 1.637643e-02
#> C[T>A]G 7.147157e-03 1.582929e-110
#> C[T>A]T 2.977982e-03 0.000000e+00
#> C[T>C]A 1.462781e-39 2.208128e-02
#> C[T>C]C 1.072073e-02 1.169024e-112
#> C[T>C]G 7.414224e-154 5.993490e-02
#> C[T>C]T 8.933946e-03 1.067777e-38
#> C[T>G]A 5.955964e-04 0.000000e+00
#> C[T>G]C 2.644202e-104 2.523575e-02
#> C[T>G]G 5.955964e-03 0.000000e+00
#> C[T>G]T 2.977982e-03 8.883300e-152
#> G[C>A]A 7.632297e-03 1.320289e-02
#> G[C>A]C 5.360367e-03 2.887238e-205
#> G[C>A]G 2.977982e-03 0.000000e+00
#> G[C>A]T 3.048468e-167 2.839022e-02
#> G[C>G]A 6.551560e-03 6.418983e-207
#> G[C>G]C 4.169175e-03 3.348432e-149
#> G[C>G]G 4.169175e-03 0.000000e+00
#> G[C>G]T 1.221315e-16 1.892681e-02
#> G[C>T]A 1.043479e-103 8.517065e-02
#> G[C>T]C 2.918422e-02 1.924785e-94
#> G[C>T]G 1.099261e-01 1.399071e-02
#> G[C>T]T 3.037542e-02 2.851360e-36
#> G[T>A]A 2.569425e-309 6.308937e-03
#> G[T>A]C 3.664590e-174 2.839022e-02
#> G[T>A]G 2.382386e-03 6.219766e-106
#> G[T>A]T 2.091409e-28 1.892681e-02
#> G[T>C]A 3.644663e-42 1.892681e-02
#> G[T>C]C 3.617385e-151 2.839022e-02
#> G[T>C]G 6.551560e-03 1.783563e-197
#> G[T>C]T 1.779025e-132 3.785362e-02
#> G[T>G]A 3.074537e-98 1.261787e-02
#> G[T>G]C 1.786789e-03 3.215628e-228
#> G[T>G]G 3.573578e-03 3.404180e-28
#> G[T>G]T 1.191193e-03 0.000000e+00
#> T[C>A]A 2.889350e-03 2.570517e-02
#> T[C>A]C 1.369872e-02 2.833485e-118
#> T[C>A]G 4.764771e-03 2.325049e-137
#> T[C>A]T 1.667670e-02 1.004236e-182
#> T[C>G]A 2.977982e-03 3.469795e-289
#> T[C>G]C 6.613130e-35 2.523575e-02
#> T[C>G]G 6.551560e-03 8.529596e-262
#> T[C>G]T 2.225880e-188 2.839022e-02
#> T[C>T]A 2.561062e-02 1.536207e-07
#> T[C>T]C 2.561064e-02 2.660370e-153
#> T[C>T]G 1.584419e-35 3.501460e-01
#> T[C>T]T 1.608110e-02 2.537158e-29
#> T[T>A]A 0.000000e+00 3.456417e-296
#> T[T>A]C 2.382386e-03 7.301042e-114
#> T[T>A]G 0.000000e+00 1.261787e-02
#> T[T>A]T 2.977982e-03 3.641266e-109
#> T[T>C]A 0.000000e+00 6.308937e-03
#> T[T>C]C 5.360367e-03 3.298783e-270
#> T[T>C]G 5.955964e-03 0.000000e+00
#> T[T>C]T 1.191193e-02 1.486345e-138
#> T[T>G]A 1.786789e-03 0.000000e+00
#> T[T>G]C 2.977982e-03 1.989832e-148
#> T[T>G]G 1.191193e-03 0.000000e+00
#> T[T>G]T 2.977982e-03 0.000000e+00
#>
#> $Exposure
#> TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806
#> Sig1 7.565056 11.144377 6.704882 12.90647 1.375751e+01
#> Sig2 1.602612 1.590532 0.000000 0.00000 2.149314e-143
#> TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812
#> Sig1 21.788890 8.523119 3.900144 11.056323 5.050140
#> Sig2 1.625003 0.000000 0.000000 1.654508 2.041469
#> TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818
#> Sig1 10.191330 5.316748 5.7395393 7.595464 9.417752
#> Sig2 3.249495 2.439561 0.9001467 1.581263 0.000000
#> TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2824
#> Sig1 10.394879 11.144377 12.0472295 17.8922669 2.8670370
#> Sig2 3.141335 1.590532 0.8665078 0.8712128 0.9264135
#> TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829
#> Sig1 9.935202e-01 3.900144 8.271511 10.2912059 9.417752
#> Sig2 5.179432e-266 0.000000 3.319841 0.8768405 0.000000
#> TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834
#> Sig1 11.9170384 1.974409 6.926579 5.682234 0
#> Sig2 0.9799417 0.000000 2.027561 1.632172 0
#> TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2841
#> Sig1 0.0000000 0.8356419 16.227792 16.26361 3.900144
#> Sig2 0.8665074 0.9866850 1.592541 0.00000 0.000000
#> TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846
#> Sig1 1.974409 6.668020 9.370132 2.943137 7.749221
#> Sig2 0.000000 2.188532 1.598945 0.000000 2.628345
#> TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853
#> Sig1 9.417752 19.586227 3.900144 4.8458470 4.652840
#> Sig2 0.000000 2.106501 0.000000 0.8665074 2.280446
#> TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859
#> Sig1 10.30313 2.943137 12.0372345 11.1795332 10.30313
#> Sig2 0.00000 0.000000 0.8753459 0.8665074 0.00000
#> TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864
#> Sig1 3.928365 15.411590 9.3686729 13.688220 10.830846
#> Sig2 3.628944 1.583421 0.9084147 1.616937 2.386487
#> TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869
#> Sig1 13.736396 0.9935202 6.647778 9.352557 8.4584162
#> Sig2 2.179991 0.0000000 2.733573 2.207129 0.9210788
#> TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874
#> Sig1 9.417752 10.551917 9.3938505 9.935202e-01 13.75751
#> Sig2 0.000000 2.003496 0.8869785 6.081454e-265 0.00000
#> TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879
#> Sig1 8.523119 7.859771 15.380805 8.457922 1.974409
#> Sig2 0.000000 2.013726 1.607035 2.206701 0.000000
#> TCGA-AB-2880 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884
#> Sig1 0.9935202 7.446140 14.60056 0.9935202 2.9068126
#> Sig2 0.0000000 1.008908 0.00000 0.0000000 0.8952299
#> TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2887 TCGA-AB-2888 TCGA-AB-2889
#> Sig1 8.427898 9.234471 10.237697 2.837042 4.845847
#> Sig2 2.225354 1.020549 2.739729 2.757865 0.000000
#> TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2892 TCGA-AB-2894 TCGA-AB-2895
#> Sig1 7.618933 12.873120 0.9935202 3.8444234 13.75751
#> Sig2 0.000000 1.589695 0.0000000 0.9110001 0.00000
#> TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900
#> Sig1 9.935202e-01 4.8187282 15.43586 8.290437 15.3422201
#> Sig2 8.087159e-265 0.8884882 0.00000 3.753497 0.9515714
#> TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906
#> Sig1 4.985998 0.9935202 19.50301 16.200047 12.016572
#> Sig2 2.080922 0.0000000 0.00000 2.209301 0.893547
#> TCGA-AB-2907 TCGA-AB-2908 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912
#> Sig1 14.60056 13.497791 9.3656766 0.000000 15.327947
#> Sig2 0.00000 2.335997 0.9109571 1.564709 2.767746
#> TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917
#> Sig1 9.353787 1.543586e+01 1.870353e+01 7.578480 10.109971
#> Sig2 2.738508 2.178232e-60 2.783721e-256 2.191001 3.292121
#> TCGA-AB-2918 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2921 TCGA-AB-2922
#> Sig1 0.9935202 8.496909 6.635605 7.578292 10.3031296
#> Sig2 0.0000000 1.583391 1.612854 0.900518 0.8665075
#> TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927
#> Sig1 1.870353e+01 8.523119 10.256387 9.385565 20.880738
#> Sig2 1.589733e-251 0.000000 2.195811 2.186317 1.058007
#> TCGA-AB-2928 TCGA-AB-2929 TCGA-AB-2930 TCGA-AB-2931 TCGA-AB-2932
#> Sig1 6.606419 13.75751 4.818730 7.527022 4.845847
#> Sig2 1.632969 0.00000 0.888487 1.629160 0.000000
#> TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937
#> Sig1 0.0000000 3.854757 3.627150 4.817387 5.669693
#> Sig2 0.8665074 2.726260 3.765531 3.204524 2.232866
#> TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 TCGA-AB-2941 TCGA-AB-2943
#> Sig1 16.26361 11.821088 1.1363803 3.8659869 13.75751
#> Sig2 0.00000 1.729667 0.7540511 0.8938488 0.00000
#> TCGA-AB-2945 TCGA-AB-2946 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949
#> Sig1 7.571351 2.701675e-121 1.974409 0.9935202 1.204723e+01
#> Sig2 1.598201 2.165931e+00 0.000000 0.0000000 3.621365e-284
#> TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956
#> Sig1 8.447855 1.290647e+01 0.0000000 1.543586e+01 2.9431367
#> Sig2 1.618128 5.350731e-321 0.8665074 5.184884e-92 0.8665074
#> TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965
#> Sig1 1.974409 14.998437 11.982753 13.736724 5.7628939
#> Sig2 0.000000 5.379565 2.207924 2.714486 0.8810699
#> TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971
#> Sig1 12.688388 6.704882 1.460056e+01 5.780637 8.5231179
#> Sig2 1.725426 0.000000 3.193239e-299 0.000000 0.8665079
#> TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2975 TCGA-AB-2976
#> Sig1 15.349214 3.900144 6.704882 0.8722250 8.383488
#> Sig2 3.687111 0.000000 0.000000 0.9592003 4.895018
#> TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981
#> Sig1 4.781991 14.139875 5.780637 4.845847 3.900144
#> Sig2 2.736504 1.263689 0.000000 0.000000 0.000000
#> TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986
#> Sig1 1.974409 9.345499 7.061468 3.900144 5.541645
#> Sig2 0.000000 2.743221 1.941213 0.000000 2.308923
#> TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991
#> Sig1 5.780637e+00 12.0270176 7.5850242 6.6699851 5.699194
#> Sig2 5.202874e-309 0.8843575 0.8949067 0.8954135 1.620623
#> TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996
#> Sig1 3.663365e-65 5.726490 7.475932 5.780637 12.842051
#> Sig2 4.461327e+00 2.198722 2.253942 0.000000 2.208296
#> TCGA-AB-2997 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001
#> Sig1 5.637528 8.523119 10.30313 2.9431367 8.427898
#> Sig2 3.262006 0.000000 0.00000 0.8665074 2.225354
#> TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008
#> Sig1 20.214553 13.697656 13.662395 4.767976 3.900144e+00
#> Sig2 2.754235 2.205679 2.228936 1.617581 4.224728e-62
#> TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012
#> Sig1 25.110309 5.780637 6.704882
#> Sig2 3.961001 0.000000 0.000000
#>
#> $Exposure.norm
#> TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806
#> Sig1 0.8251887 0.8751046 1 1 1.000000e+00
#> Sig2 0.1748113 0.1248954 0 0 1.562284e-144
#> TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812
#> Sig1 0.93059662 1 1 0.8698348 0.7121289
#> Sig2 0.06940338 0 0 0.1301652 0.2878711
#> TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818
#> Sig1 0.7582369 0.685474 0.8644293 0.8276877 1
#> Sig2 0.2417631 0.314526 0.1355707 0.1723123 0
#> TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2824
#> Sig1 0.767931 0.8751046 0.93290031 0.9535687 0.7557861
#> Sig2 0.232069 0.1248954 0.06709969 0.0464313 0.2442139
#> TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829
#> Sig1 1.000000e+00 1 0.7135933 0.92148667 1
#> Sig2 5.213213e-266 0 0.2864067 0.07851333 0
#> TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834
#> Sig1 0.92401774 1 0.7735616 0.7768552 NaN
#> Sig2 0.07598226 0 0.2264384 0.2231448 NaN
#> TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2841
#> Sig1 0 0.4585576 0.91063347 1 1
#> Sig2 1 0.5414424 0.08936653 0 0
#> TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846
#> Sig1 1 0.7528912 0.8542316 1 0.7467282
#> Sig2 0 0.2471088 0.1457684 0 0.2532718
#> TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853
#> Sig1 1 0.90289369 1 0.8483099 0.6710873
#> Sig2 0 0.09710631 0 0.1516901 0.3289127
#> TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859
#> Sig1 1 1 0.93220984 0.92806704 1
#> Sig2 0 0 0.06779016 0.07193296 0
#> TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864
#> Sig1 0.5198101 0.90683024 0.91160777 0.8943534 0.8194427
#> Sig2 0.4801899 0.09316976 0.08839223 0.1056466 0.1805573
#> TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869
#> Sig1 0.8630348 1 0.7086163 0.8090667 0.90179868
#> Sig2 0.1369652 0 0.2913837 0.1909333 0.09820132
#> TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874
#> Sig1 1 0.8404277 0.913725 1.000000e+00 1
#> Sig2 0 0.1595723 0.086275 6.121117e-265 0
#> TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879
#> Sig1 1 0.7960473 0.90540088 0.7930822 1
#> Sig2 0 0.2039527 0.09459912 0.2069178 0
#> TCGA-AB-2880 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884
#> Sig1 1 0.8806739 1 1 0.7645397
#> Sig2 0 0.1193261 0 0 0.2354603
#> TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2887 TCGA-AB-2888 TCGA-AB-2889
#> Sig1 0.7911103 0.90048298 0.788885 0.5070758 1
#> Sig2 0.2088897 0.09951702 0.211115 0.4929242 0
#> TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2892 TCGA-AB-2894 TCGA-AB-2895
#> Sig1 1 0.890084 1 0.8084292 1
#> Sig2 0 0.109916 0 0.1915708 0
#> TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900
#> Sig1 1.000000e+00 0.844322 1 0.6883496 0.94159914
#> Sig2 8.139904e-265 0.155678 0 0.3116504 0.05840086
#> TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906
#> Sig1 0.7055405 1 1 0.8799902 0.93078708
#> Sig2 0.2944595 0 0 0.1200098 0.06921292
#> TCGA-AB-2907 TCGA-AB-2908 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912
#> Sig1 1 0.8524676 0.91135647 0 0.8470495
#> Sig2 0 0.1475324 0.08864353 1 0.1529505
#> TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917
#> Sig1 0.7735328 1.000000e+00 1.00000e+00 0.77573 0.7543577
#> Sig2 0.2264672 1.411151e-61 1.48834e-257 0.22427 0.2456423
#> TCGA-AB-2918 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2921 TCGA-AB-2922
#> Sig1 1 0.8429223 0.804466 0.8937919 0.92242295
#> Sig2 0 0.1570777 0.195534 0.1062081 0.07757705
#> TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927
#> Sig1 1.00000e+00 1 0.8236608 0.8110664 0.95177448
#> Sig2 8.49964e-253 0 0.1763392 0.1889336 0.04822552
#> TCGA-AB-2928 TCGA-AB-2929 TCGA-AB-2930 TCGA-AB-2931 TCGA-AB-2932
#> Sig1 0.8018095 1 0.8443222 0.8220699 1
#> Sig2 0.1981905 0 0.1556778 0.1779301 0
#> TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937
#> Sig1 0 0.5857388 0.4906407 0.6005286 0.7174502
#> Sig2 1 0.4142612 0.5093593 0.3994714 0.2825498
#> TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 TCGA-AB-2941 TCGA-AB-2943
#> Sig1 1 0.8723564 0.6011222 0.8122102 1
#> Sig2 0 0.1276436 0.3988778 0.1877898 0
#> TCGA-AB-2945 TCGA-AB-2946 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949
#> Sig1 0.8257057 1.24735e-121 1 1 1.000000e+00
#> Sig2 0.1742943 1.00000e+00 0 0 3.005974e-285
#> TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956
#> Sig1 0.8392479 1.000000e+00 0 1.000000e+00 0.772549
#> Sig2 0.1607521 4.150151e-322 1 3.358986e-93 0.227451
#> TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965
#> Sig1 1 0.7360112 0.8444102 0.8349978 0.8673879
#> Sig2 0 0.2639888 0.1555898 0.1650022 0.1326121
#> TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971
#> Sig1 0.8802936 1 1.000000e+00 1 0.90771646
#> Sig2 0.1197064 0 2.187065e-300 0 0.09228354
#> TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2975 TCGA-AB-2976
#> Sig1 0.8063118 1 1 0.4762548 0.6313578
#> Sig2 0.1936882 0 0 0.5237452 0.3686422
#> TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981
#> Sig1 0.6360303 0.91796125 1 1 1
#> Sig2 0.3639697 0.08203875 0 0 0
#> TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986
#> Sig1 1 0.773076 0.7843739 1 0.705891
#> Sig2 0 0.226924 0.2156261 0 0.294109
#> TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991
#> Sig1 1.000000e+00 0.93150555 0.8944677 0.8816436 0.7785979
#> Sig2 9.000521e-310 0.06849445 0.1055323 0.1183564 0.2214021
#> TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996
#> Sig1 8.211379e-66 0.7225662 0.7683483 1 0.8532727
#> Sig2 1.000000e+00 0.2774338 0.2316517 0 0.1467273
#> TCGA-AB-2997 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001
#> Sig1 0.6334632 1 1 0.772549 0.7911103
#> Sig2 0.3665368 0 0 0.227451 0.2088897
#> TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008
#> Sig1 0.8800879 0.8613071 0.8597389 0.7466813 1.000000e+00
#> Sig2 0.1199121 0.1386929 0.1402611 0.2533187 1.083224e-62
#> TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012
#> Sig1 0.8637488 1 1
#> Sig2 0.1362512 0 0
#>
#> $K
#> [1] 2
#>
#> $Raw
#> $Raw$summary_run
#> # A tibble: 3 × 5
#> Run K posterior file similarity_to_ref
#> <int> <int> <dbl> <chr> <dbl>
#> 1 2 2 9714. /tmp/RtmpT86DiN/BayesNMF.2.rds 0.718
#> 2 3 2 9711. /tmp/RtmpT86DiN/BayesNMF.3.rds 0.676
#> 3 1 3 9676. /tmp/RtmpT86DiN/BayesNMF.1.rds 0.611
#>
#> $Raw$W
#> Sig1 Sig2
#> A[C>A]A 2.649894e-01 1.215678e-44
#> A[C>A]C 4.520407e-01 6.201727e-148
#> A[C>A]G 6.235044e-02 0.000000e+00
#> A[C>A]T 7.325113e-103 2.040114e-01
#> A[C>G]A 2.182266e-01 1.891007e-15
#> A[C>G]C 9.352567e-02 6.489727e-44
#> A[C>G]G 1.247009e-01 2.400511e-296
#> A[C>G]T 1.247009e-01 6.035016e-94
#> A[C>T]A 7.949682e-01 9.087293e-101
#> A[C>T]C 7.949682e-01 1.219569e-111
#> A[C>T]G 3.600738e+00 7.417795e-72
#> A[C>T]T 4.052779e-01 9.040417e-143
#> A[T>A]A 7.434535e-171 9.591072e-76
#> A[T>A]C 1.870513e-01 8.962249e-102
#> A[T>A]G 4.210896e-129 1.530086e-01
#> A[T>A]T 6.235044e-02 2.506395e-320
#> A[T>C]A 4.364531e-01 6.834930e-78
#> A[T>C]C 1.870513e-01 3.590594e-11
#> A[T>C]G 4.208654e-01 2.296281e-07
#> A[T>C]T 4.832159e-01 8.420791e-24
#> A[T>G]A 9.352567e-02 4.965744e-55
#> A[T>G]C 0.000000e+00 5.100285e-02
#> A[T>G]G 4.676283e-02 3.358751e-135
#> A[T>G]T 4.676283e-02 5.462850e-244
#> C[C>A]A 2.805770e-01 0.000000e+00
#> C[C>A]C 6.339286e-124 3.825214e-01
#> C[C>A]G 2.182266e-01 2.069643e-239
#> C[C>A]T 2.805770e-01 9.740311e-72
#> C[C>G]A 2.026389e-01 2.642810e-16
#> C[C>G]C 6.235044e-02 0.000000e+00
#> C[C>G]G 2.338133e-01 1.427795e-06
#> C[C>G]T 1.091133e-01 4.505137e-22
#> C[C>T]A 6.390921e-01 2.727189e-245
#> C[C>T]C 4.676283e-01 1.325265e-124
#> C[C>T]G 3.101163e+00 1.542714e-01
#> C[C>T]T 9.352567e-01 4.910624e-90
#> C[T>A]A 8.957060e-106 4.175109e-90
#> C[T>A]C 7.495298e-02 1.323907e-01
#> C[T>A]G 1.870513e-01 1.279675e-109
#> C[T>A]T 7.793806e-02 0.000000e+00
#> C[T>C]A 3.828307e-38 1.785100e-01
#> C[T>C]C 2.805770e-01 9.450653e-112
#> C[T>C]G 1.940409e-152 4.845271e-01
#> C[T>C]T 2.338142e-01 8.632143e-38
#> C[T>G]A 1.558761e-02 0.000000e+00
#> C[T>G]C 6.920257e-103 2.040114e-01
#> C[T>G]G 1.558761e-01 0.000000e+00
#> C[T>G]T 7.793806e-02 7.181457e-151
#> G[C>A]A 1.997481e-01 1.067351e-01
#> G[C>A]C 1.402885e-01 2.334107e-204
#> G[C>A]G 7.793806e-02 0.000000e+00
#> G[C>A]T 7.978279e-166 2.295128e-01
#> G[C>G]A 1.714637e-01 5.189249e-206
#> G[C>G]C 1.091133e-01 2.706947e-148
#> G[C>G]G 1.091133e-01 0.000000e+00
#> G[C>G]T 3.196356e-15 1.530086e-01
#> G[C>T]A 2.730935e-102 6.885385e-01
#> G[C>T]C 7.637929e-01 1.556039e-93
#> G[C>T]G 2.876924e+00 1.131040e-01
#> G[C>T]T 7.949682e-01 2.305103e-35
#> G[T>A]A 6.724555e-308 5.100285e-02
#> G[T>A]C 9.590757e-173 2.295128e-01
#> G[T>A]G 6.235044e-02 5.028197e-105
#> G[T>A]T 5.473518e-27 1.530086e-01
#> G[T>C]A 9.538606e-41 1.530086e-01
#> G[T>C]C 9.467214e-150 2.295128e-01
#> G[T>C]G 1.714637e-01 1.441872e-196
#> G[T>C]T 4.655964e-131 3.060171e-01
#> G[T>G]A 8.046505e-97 1.020057e-01
#> G[T>G]C 4.676283e-02 2.599585e-227
#> G[T>G]G 9.352567e-02 2.752015e-27
#> G[T>G]T 3.117522e-02 0.000000e+00
#> T[C>A]A 7.561843e-02 2.078063e-01
#> T[C>A]C 3.585151e-01 2.290652e-117
#> T[C>A]G 1.247009e-01 1.879621e-136
#> T[C>A]T 4.364531e-01 8.118464e-182
#> T[C>G]A 7.793806e-02 2.805059e-288
#> T[C>G]C 1.730751e-33 2.040114e-01
#> T[C>G]G 1.714637e-01 6.895515e-261
#> T[C>G]T 5.825448e-187 2.295128e-01
#> T[C>T]A 6.702665e-01 1.241904e-06
#> T[C>T]C 6.702673e-01 2.150703e-152
#> T[C>T]G 4.146651e-34 2.830658e+00
#> T[C>T]T 4.208655e-01 2.051095e-28
#> T[T>A]A 0.000000e+00 2.794244e-295
#> T[T>A]C 6.235044e-02 5.902324e-113
#> T[T>A]G 0.000000e+00 1.020057e-01
#> T[T>A]T 7.793806e-02 2.943680e-108
#> T[T>C]A 0.000000e+00 5.100285e-02
#> T[T>C]C 1.402885e-01 2.666809e-269
#> T[T>C]G 1.558761e-01 0.000000e+00
#> T[T>C]T 3.117522e-01 1.201594e-137
#> T[T>G]A 4.676283e-02 0.000000e+00
#> T[T>G]C 7.793806e-02 1.608625e-147
#> T[T>G]G 3.117522e-02 0.000000e+00
#> T[T>G]T 7.793806e-02 0.000000e+00
#>
#> $Raw$H
#> TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806
#> Sig1 0.2890578 0.4258222 0.2561909 0.4931512 5.256689e-01
#> Sig2 0.1982395 0.1967452 0.0000000 0.0000000 2.658653e-144
#> TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812
#> Sig1 0.8325448 0.3256649 0.1490229 0.4224577 0.1929638
#> Sig2 0.2010092 0.0000000 0.0000000 0.2046589 0.2525252
#> TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818
#> Sig1 0.3894066 0.2031508 0.2193055 0.2902196 0.3598485
#> Sig2 0.4019552 0.3017682 0.1113461 0.1955987 0.0000000
#> TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2824
#> Sig1 0.3971842 0.4258222 0.4603198 0.6836564 0.1095483
#> Sig2 0.3885760 0.1967452 0.1071850 0.1077670 0.1145953
#> TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829
#> Sig1 3.796201e-02 0.1490229 0.3160511 0.3932229 0.3598485
#> Sig2 6.406840e-267 0.0000000 0.4106568 0.1084632 0.0000000
#> TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834
#> Sig1 0.4553453 0.07544138 0.2646618 0.2171159 0
#> Sig2 0.1212166 0.00000000 0.2508047 0.2018960 0
#> TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2841
#> Sig1 0.000000 0.03192954 0.6200574 0.621426 0.1490229
#> Sig2 0.107185 0.12205070 0.1969938 0.000000 0.0000000
#> TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846
#> Sig1 0.07544138 0.2547824 0.3580290 0.1124561 0.2960946
#> Sig2 0.00000000 0.2707165 0.1977859 0.0000000 0.3251203
#> TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853
#> Sig1 0.3598485 0.7483819 0.1490229 0.1851579 0.1777832
#> Sig2 0.0000000 0.2605694 0.0000000 0.1071850 0.2820860
#> TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859
#> Sig1 0.3936785 0.1124561 0.4599379 0.4271655 0.3936785
#> Sig2 0.0000000 0.0000000 0.1082783 0.1071850 0.0000000
#> TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864
#> Sig1 0.1501013 0.5888707 0.3579732 0.5230214 0.4138423
#> Sig2 0.4488921 0.1958656 0.1123688 0.2000115 0.2952030
#> TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869
#> Sig1 0.5248622 0.03796201 0.2540089 0.3573575 0.3231927
#> Sig2 0.2696600 0.00000000 0.3381368 0.2730168 0.1139354
#> TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874
#> Sig1 0.3598485 0.4031845 0.3589353 3.796201e-02 0.5256689
#> Sig2 0.0000000 0.2478279 0.1097172 7.522621e-266 0.0000000
#> TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879
#> Sig1 0.3256649 0.3003187 0.5876944 0.3231738 0.07544138
#> Sig2 0.0000000 0.2490934 0.1987865 0.2729639 0.00000000
#> TCGA-AB-2880 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884
#> Sig1 0.03796201 0.2845140 0.5578817 0.03796201 0.1110681
#> Sig2 0.00000000 0.1247996 0.0000000 0.00000000 0.1107379
#> TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2887 TCGA-AB-2888 TCGA-AB-2889
#> Sig1 0.3220266 0.3528454 0.3911783 0.1084022 0.1851579
#> Sig2 0.2752713 0.1262396 0.3388982 0.3411417 0.0000000
#> TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2892 TCGA-AB-2894 TCGA-AB-2895
#> Sig1 0.2911164 0.4918767 0.03796201 0.1468939 0.5256689
#> Sig2 0.0000000 0.1966417 0.00000000 0.1126887 0.0000000
#> TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900
#> Sig1 3.796201e-02 0.1841217 0.589798 0.3167743 0.5862201
#> Sig2 1.000363e-265 0.1099040 0.000000 0.4642991 0.1177072
#> TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906
#> Sig1 0.1905130 0.03796201 0.7452021 0.6189973 0.4591484
#> Sig2 0.2574053 0.00000000 0.0000000 0.2732856 0.1105297
#> TCGA-AB-2907 TCGA-AB-2908 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912
#> Sig1 0.5578817 0.5157452 0.3578588 0.000000 0.5856747
#> Sig2 0.0000000 0.2889575 0.1126833 0.193551 0.3423639
#> TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917
#> Sig1 0.3574045 5.897980e-01 7.146543e-01 0.2895707 0.3862979
#> Sig2 0.3387473 2.694424e-61 3.443400e-257 0.2710219 0.4072280
#> TCGA-AB-2918 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2921 TCGA-AB-2922
#> Sig1 0.03796201 0.3246635 0.2535438 0.2895635 0.3936785
#> Sig2 0.00000000 0.1958618 0.1995064 0.1113920 0.1071850
#> TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927
#> Sig1 7.146543e-01 0.3256649 0.3918924 0.3586187 0.7978446
#> Sig2 1.966463e-252 0.0000000 0.2716169 0.2704425 0.1308731
#> TCGA-AB-2928 TCGA-AB-2929 TCGA-AB-2930 TCGA-AB-2931 TCGA-AB-2932
#> Sig1 0.2524286 0.5256689 0.1841217 0.2876045 0.1851579
#> Sig2 0.2019945 0.0000000 0.1099038 0.2015234 0.0000000
#> TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937
#> Sig1 0.000000 0.1472887 0.1385919 0.1840704 0.2166367
#> Sig2 0.107185 0.3372322 0.4657877 0.3963923 0.2762005
#> TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 TCGA-AB-2941 TCGA-AB-2943
#> Sig1 0.621426 0.4516790 0.04342063 0.1477178 0.5256689
#> Sig2 0.000000 0.2139559 0.09327441 0.1105671 0.0000000
#> TCGA-AB-2945 TCGA-AB-2946 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949
#> Sig1 0.2892983 1.032299e-122 0.07544138 0.03796201 4.603198e-01
#> Sig2 0.1976939 2.679208e-01 0.00000000 0.00000000 4.479547e-285
#> TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956
#> Sig1 0.3227892 4.931512e-01 0.000000 5.897980e-01 0.1124561
#> Sig2 0.2001588 6.620480e-322 0.107185 6.413585e-93 0.1071850
#> TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965
#> Sig1 0.07544138 0.5730843 0.4578562 0.5248747 0.2201979
#> Sig2 0.00000000 0.6654400 0.2731152 0.3357758 0.1089864
#> TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971
#> Sig1 0.4848182 0.2561909 5.578817e-01 0.2208758 0.3256649
#> Sig2 0.2134313 0.0000000 3.949964e-300 0.0000000 0.1071851
#> TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2975 TCGA-AB-2976
#> Sig1 0.5864873 0.1490229 0.2561909 0.03332737 0.3203297
#> Sig2 0.4560873 0.0000000 0.0000000 0.11865091 0.6055026
#> TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981
#> Sig1 0.1827180 0.5402790 0.2208758 0.1851579 0.1490229
#> Sig2 0.3384994 0.1563155 0.0000000 0.0000000 0.0000000
#> TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986
#> Sig1 0.07544138 0.3570878 0.2698159 0.1490229 0.2117440
#> Sig2 0.00000000 0.3393302 0.2401237 0.0000000 0.2856086
#> TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991
#> Sig1 2.208758e-01 0.4595475 0.2898207 0.2548575 0.2177639
#> Sig2 6.435837e-310 0.1093930 0.1106979 0.1107606 0.2004674
#> TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996
#> Sig1 1.399757e-66 0.2188069 0.2856524 0.2208758 0.4906896
#> Sig2 5.518561e-01 0.2719770 0.2788075 0.0000000 0.2731613
#> TCGA-AB-2997 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001
#> Sig1 0.2154077 0.3256649 0.3936785 0.1124561 0.3220266
#> Sig2 0.4035028 0.0000000 0.0000000 0.1071850 0.2752713
#> TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008
#> Sig1 0.7723900 0.5233819 0.5220347 0.1821824 1.490229e-01
#> Sig2 0.3406926 0.2728375 0.2757143 0.2000911 5.225893e-63
#> TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012
#> Sig1 0.9594549 0.2208758 0.2561909
#> Sig2 0.4899668 0.0000000 0.0000000
#>
#> $Raw$best_run
#> [1] 2
#>
#>
#> attr(,"class")
#> [1] "Signature"
#> attr(,"nrun")
#> [1] 3
#> attr(,"method")
#> [1] "L1W.L2H"
#> attr(,"call_method")
#> [1] "BayesianNMF"
# }