The function performs a signatures decomposition of a given mutational
catalogue V with known signatures W by solving the minimization problem
min(||W*H - V||) where W and V are known.
sig_fit(
catalogue_matrix,
sig,
sig_index = NULL,
sig_db = c("legacy", "SBS", "DBS", "ID", "TSB", "SBS_Nik_lab", "RS_Nik_lab",
"RS_BRCA560", "RS_USARC", "CNS_USARC", "CNS_TCGA", "CNS_TCGA176", "CNS_PCAWG176",
"SBS_hg19", "SBS_hg38", "SBS_mm9", "SBS_mm10", "DBS_hg19", "DBS_hg38", "DBS_mm9",
"DBS_mm10", "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ", "latest_SBS_GRCh37",
"latest_DBS_GRCh37", "latest_ID_GRCh37", "latest_SBS_GRCh38", "latest_DBS_GRCh38",
"latest_SBS_mm9", "latest_DBS_mm9", "latest_SBS_mm10", "latest_DBS_mm10",
"latest_SBS_rn6", "latest_DBS_rn6", "latest_CN_GRCh37",
"latest_RNA-SBS_GRCh37", "latest_SV_GRCh38"),
db_type = c("", "human-exome", "human-genome"),
show_index = TRUE,
method = c("QP", "NNLS", "SA"),
auto_reduce = FALSE,
type = c("absolute", "relative"),
return_class = c("matrix", "data.table"),
return_error = FALSE,
rel_threshold = 0,
mode = c("SBS", "DBS", "ID", "copynumber"),
true_catalog = NULL,
...
)Arguments
- catalogue_matrix
a numeric matrix
Vwith row representing components and columns representing samples, typically you can getnmf_matrixfromsig_tally()and transpose it byt().- sig
a
Signatureobject obtained either from sig_extract or sig_auto_extract, or just a raw signature matrix/data.framewith row representing components (motifs) and column representing signatures.- sig_index
a vector for signature index. "ALL" for all signatures.
- sig_db
default 'legacy', it can be 'legacy' (for COSMIC v2 'SBS'), 'SBS', 'DBS', 'ID' and 'TSB' (for COSMIV v3.1 signatures) for small scale mutations. For more specific details, it can also be 'SBS_hg19', 'SBS_hg38', 'SBS_mm9', 'SBS_mm10', 'DBS_hg19', 'DBS_hg38', 'DBS_mm9', 'DBS_mm10' to use COSMIC v3 reference signatures from Alexandrov, Ludmil B., et al. (2020) (reference #1). In addition, it can be one of "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ", "SBS_Nik_lab", "RS_Nik_lab" to refer reference signatures from Degasperi, Andrea, et al. (2020) (reference #2); "RS_BRCA560", "RS_USARC" to reference signatures from BRCA560 and USARC cohorts; "CNS_USARC" (40 categories), "CNS_TCGA" (48 categories) to reference copy number signatures from USARC cohort and TCGA; "CNS_TCGA176" (176 categories) and "CNS_PCAWG176" (176 categories) to reference copy number signatures from PCAWG and TCGA separately. UPDATE, the latest version of reference version can be automatically downloaded and loaded from https://cancer.sanger.ac.uk/signatures/downloads/ when a option with
latest_prefix is specified (e.g. "latest_SBS_GRCh37"). Note: the signature profile for different genome builds are basically same. And specific database (e.g. 'SBS_mm10') contains less signatures than all COSMIC signatures (because some signatures are not detected from Alexandrov, Ludmil B., et al. (2020)). For all available options, check the parameter setting.- db_type
only used when
sig_dbis enabled. "" for keeping default, "human-exome" for transforming to exome frequency of component, and "human-genome" for transforming to whole genome frequency of component. Currently only works for 'SBS'.- show_index
if
TRUE, show valid indices.- method
method to solve the minimazation problem. 'NNLS' for non-negative least square; 'QP' for quadratic programming; 'SA' for simulated annealing.
- auto_reduce
if
TRUE, try reducing the input reference signatures to increase the cosine similarity of reconstructed profile to observed profile.- type
'absolute' for signature exposure and 'relative' for signature relative exposure.
- return_class
string, 'matrix' or 'data.table'.
- return_error
if
TRUE, also return sample error (Frobenius norm) and cosine similarity between observed sample profile (asa. spectrum) and reconstructed profile. NOTE: it is better to obtain the error when the type is 'absolute', because the error is affected by relative exposure accuracy.- rel_threshold
numeric vector, a signature with relative exposure lower than (equal is included, i.e.
<=) this value will be set to 0 (both absolute exposure and relative exposure). In this case, sum of signature contribution may not equal to 1.- mode
signature type for plotting, now supports 'copynumber', 'SBS', 'DBS', 'ID' and 'RS' (genome rearrangement signature).
- true_catalog
used by sig_fit_bootstrap, user never use it.
- ...
control parameters passing to argument
controlinGenSAfunction when use method 'SA'.
Value
The exposure result either in matrix or data.table format.
If return_error set TRUE, a list is returned.
Details
The method 'NNLS' solves the minimization problem with nonnegative least-squares constraints. The method 'QP' and 'SA' are modified from SignatureEstimation package. See references for details. Of note, when fitting exposures for copy number signatures, only components of feature CN is used.
References
Daniel Huebschmann, Zuguang Gu and Matthias Schlesner (2019). YAPSA: Yet Another Package for Signature Analysis. R package version 1.12.0.
Huang X, Wojtowicz D, Przytycka TM. Detecting presence of mutational signatures in cancer with confidence. Bioinformatics. 2018;34(2):330–337. doi:10.1093/bioinformatics/btx604
Kim, Jaegil, et al. "Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors." Nature genetics 48.6 (2016): 600.
Examples
# \donttest{
# For mutational signatures ----------------
# SBS is used for illustration, similar
# operations can be applied to DBS, INDEL, CN, RS, etc.
# Load simulated data
data("simulated_catalogs")
data = simulated_catalogs$set1
data[1:5, 1:5]
#> Sample_1 Sample_2 Sample_3 Sample_4 Sample_5
#> A[C>A]A 911 195 95 131 33
#> A[C>A]C 761 175 51 71 10
#> A[C>A]G 88 19 12 14 2
#> A[C>A]T 744 174 55 77 14
#> C[C>A]A 883 225 142 170 55
# Fitting with all COSMIC v2 reference signatures
sig_fit(data, sig_index = "ALL")
#> ℹ [2024-08-04 14:44:52.714294]: Started.
#> ✔ [2024-08-04 14:44:52.716068]: Signature index detected.
#> ℹ [2024-08-04 14:44:52.717448]: Checking signature database in package.
#> ℹ [2024-08-04 14:44:52.71987]: Checking signature index.
#> ℹ [2024-08-04 14:44:52.721265]: Valid index for db 'legacy':
#> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
#> ✔ [2024-08-04 14:44:52.722724]: Database and index checked.
#> ✔ [2024-08-04 14:44:52.724327]: Signature normalized.
#> ℹ [2024-08-04 14:44:52.725697]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:52.727009]: Checked.
#> ℹ [2024-08-04 14:44:52.728322]: Checking rownames for catalog matrix and signature matrix.
#> ℹ [2024-08-04 14:44:52.729666]: Matrix V and W don't have same orders. Try reordering...
#> ✔ [2024-08-04 14:44:52.7311]: Checked.
#> ✔ [2024-08-04 14:44:52.732512]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:52.733961]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:52.7353]: Calling function.
#> ℹ [2024-08-04 14:44:52.737009]: Fitting sample: Sample_1
#> ℹ [2024-08-04 14:44:52.738683]: Fitting sample: Sample_2
#> ℹ [2024-08-04 14:44:52.740212]: Fitting sample: Sample_3
#> ℹ [2024-08-04 14:44:52.741813]: Fitting sample: Sample_4
#> ℹ [2024-08-04 14:44:52.743363]: Fitting sample: Sample_5
#> ℹ [2024-08-04 14:44:52.744917]: Fitting sample: Sample_6
#> ℹ [2024-08-04 14:44:52.746477]: Fitting sample: Sample_7
#> ℹ [2024-08-04 14:44:52.747995]: Fitting sample: Sample_8
#> ℹ [2024-08-04 14:44:52.749542]: Fitting sample: Sample_9
#> ℹ [2024-08-04 14:44:52.751054]: Fitting sample: Sample_10
#> ℹ [2024-08-04 14:44:52.752588]: Fitting sample: Sample_11
#> ℹ [2024-08-04 14:44:52.754441]: Fitting sample: Sample_12
#> ℹ [2024-08-04 14:44:52.755956]: Fitting sample: Sample_13
#> ℹ [2024-08-04 14:44:52.757516]: Fitting sample: Sample_14
#> ℹ [2024-08-04 14:44:52.759066]: Fitting sample: Sample_15
#> ℹ [2024-08-04 14:44:52.760595]: Fitting sample: Sample_16
#> ℹ [2024-08-04 14:44:52.762135]: Fitting sample: Sample_17
#> ℹ [2024-08-04 14:44:52.76365]: Fitting sample: Sample_18
#> ℹ [2024-08-04 14:44:52.765161]: Fitting sample: Sample_19
#> ℹ [2024-08-04 14:44:52.766698]: Fitting sample: Sample_20
#> ℹ [2024-08-04 14:44:52.768184]: Fitting sample: Sample_21
#> ℹ [2024-08-04 14:44:52.769712]: Fitting sample: Sample_22
#> ℹ [2024-08-04 14:44:52.771227]: Fitting sample: Sample_23
#> ℹ [2024-08-04 14:44:52.772797]: Fitting sample: Sample_24
#> ℹ [2024-08-04 14:44:52.774349]: Fitting sample: Sample_25
#> ℹ [2024-08-04 14:44:52.775883]: Fitting sample: Sample_26
#> ℹ [2024-08-04 14:44:52.777424]: Fitting sample: Sample_27
#> ℹ [2024-08-04 14:44:52.778927]: Fitting sample: Sample_28
#> ℹ [2024-08-04 14:44:52.780445]: Fitting sample: Sample_29
#> ℹ [2024-08-04 14:44:52.781975]: Fitting sample: Sample_30
#> ✔ [2024-08-04 14:44:52.783481]: Done.
#> ℹ [2024-08-04 14:44:52.784839]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:52.787091]: Done.
#> ℹ [2024-08-04 14:44:52.788568]: 0.074 secs elapsed.
#> Sample_1 Sample_2 Sample_3 Sample_4 Sample_5
#> COSMIC_1 0.000000 0.000000 12.316692 0.000000 0.000000
#> COSMIC_2 0.000000 3349.510152 0.000000 0.000000 948.379212
#> COSMIC_3 13596.457821 0.000000 6.574699 1755.900808 125.782093
#> COSMIC_4 15.264857 0.000000 2.708319 0.000000 0.000000
#> COSMIC_5 88.759109 0.000000 3035.361542 1671.687846 0.000000
#> COSMIC_6 50.489937 3138.613536 3408.708042 0.000000 0.000000
#> COSMIC_7 0.000000 0.000000 0.000000 0.780399 0.322276
#> COSMIC_8 13410.973058 4399.640806 5.111720 0.502994 0.000000
#> COSMIC_9 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_10 2.502093 0.000000 0.000000 0.000000 2.649920
#> COSMIC_11 0.000000 0.000000 0.000000 0.000000 0.628539
#> COSMIC_12 14636.867322 3173.628918 1112.660642 2644.810440 0.000000
#> COSMIC_13 3.345820 4740.202983 2489.698611 3604.349332 1027.188236
#> COSMIC_14 0.000000 7.622208 1.644765 0.000000 0.000000
#> COSMIC_15 0.000000 0.000000 6.356134 0.542811 0.000000
#> COSMIC_16 10.838333 0.000000 3.569317 2.729935 0.000000
#> COSMIC_17 788.136285 0.000000 0.000000 0.000000 11.345102
#> COSMIC_18 0.000000 0.000000 660.528061 890.441688 557.937060
#> COSMIC_19 0.000000 0.750380 5.703897 2.305603 0.000000
#> COSMIC_20 0.000000 0.000000 11.826130 0.000000 0.000000
#> COSMIC_21 19.999782 0.605214 0.000000 0.000000 0.000000
#> COSMIC_22 0.000000 1.412315 2.326967 1.470566 0.000000
#> COSMIC_23 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_24 0.000000 0.000000 0.000000 0.000000 1.734102
#> COSMIC_25 0.000000 2.339510 0.000000 0.000000 0.000000
#> COSMIC_26 0.000000 5.829081 0.000000 10.477579 0.000000
#> COSMIC_27 0.000000 0.690230 0.413775 0.000000 0.617212
#> COSMIC_28 128.579595 3.154668 0.000000 0.000000 11.570903
#> COSMIC_29 7.785988 0.000000 0.000000 0.000000 6.845345
#> COSMIC_30 0.000000 0.000000 4.490687 0.000000 0.000000
#> Sample_6 Sample_7 Sample_8 Sample_9 Sample_10 Sample_11
#> COSMIC_1 1.593571 4.880078 1236.351733 0.000000 1.014648 878.357543
#> COSMIC_2 447.638410 0.000000 239.380593 0.000000 1325.806777 624.216936
#> COSMIC_3 287.957097 0.000000 294.616206 1910.527717 1527.088437 5.201832
#> COSMIC_4 0.115174 0.000000 0.000000 0.344221 0.000000 4.241885
#> COSMIC_5 0.000000 336.238603 97.850592 1253.756212 3348.758707 2309.500447
#> COSMIC_6 351.904226 253.679248 0.000000 72.341307 0.000000 646.758198
#> COSMIC_7 0.000000 0.000000 1.451300 1.291309 1.070439 0.000000
#> COSMIC_8 243.207761 4.231027 0.000000 0.000000 2518.120558 0.000000
#> COSMIC_9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_10 0.105083 0.000000 0.000000 0.565740 0.652112 0.000000
#> COSMIC_11 1.573701 0.000000 0.000000 0.000000 0.395463 0.000000
#> COSMIC_12 0.000000 1.558663 2.680746 0.000000 0.000000 9.303593
#> COSMIC_13 0.412038 399.409491 0.000000 711.486825 0.000000 746.132722
#> COSMIC_14 0.036217 1.724017 0.000000 0.322584 0.000000 0.000000
#> COSMIC_15 0.000000 1.955241 0.000000 2.737638 1.470945 3.294826
#> COSMIC_16 0.000000 0.000000 0.000000 7.874248 0.000000 6.060704
#> COSMIC_17 0.000000 162.051155 0.000000 4107.930816 0.000000 0.000000
#> COSMIC_18 262.002399 429.270451 508.415723 0.000000 978.795305 1.757806
#> COSMIC_19 0.000000 0.000000 0.000000 0.000000 1.812196 4.046976
#> COSMIC_20 0.000000 0.000000 2.418327 0.000000 0.000000 4.132387
#> COSMIC_21 0.000000 1.423649 0.000000 0.000000 0.000000 0.000000
#> COSMIC_22 0.000000 0.000000 0.000000 0.000000 0.000000 1.185078
#> COSMIC_23 0.000000 0.000000 0.000000 1.486023 0.000000 0.000000
#> COSMIC_24 0.690493 0.070519 0.000000 0.000000 0.000000 0.000000
#> COSMIC_25 0.000000 0.000000 0.000000 0.000000 1.230116 0.761657
#> COSMIC_26 0.000000 0.507859 0.000000 0.000000 0.000000 4.676707
#> COSMIC_27 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_28 7.940466 0.000000 8.063004 49.575537 6.784297 0.000000
#> COSMIC_29 7.823365 0.000000 0.771775 3.759826 0.000000 0.000000
#> COSMIC_30 0.000000 0.000000 0.000000 0.000000 0.000000 6.370705
#> Sample_12 Sample_13 Sample_14 Sample_15 Sample_16
#> COSMIC_1 6.837473 2.883482 1.812292 508.701296 0.000000
#> COSMIC_2 0.000000 0.366162 1119.406113 0.000000 0.000000
#> COSMIC_3 15860.219425 4.421433 6.574966 18.115040 1677.967550
#> COSMIC_4 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_5 6692.477024 0.000000 1074.779287 4438.808139 334.878313
#> COSMIC_6 0.000000 88.673686 158.223498 0.000000 0.000000
#> COSMIC_7 0.000000 0.498306 0.216809 0.000000 0.000000
#> COSMIC_8 9.812595 427.338774 0.000000 12.690741 2.945048
#> COSMIC_9 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_10 0.000000 0.306919 0.000000 0.000000 1.439702
#> COSMIC_11 0.000000 0.000000 0.000000 1.578921 0.000000
#> COSMIC_12 12747.006106 510.641670 998.007438 23.461748 1867.930943
#> COSMIC_13 4219.832742 725.821797 826.863849 3260.970572 698.766395
#> COSMIC_14 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_15 0.862951 0.343456 0.000000 0.153861 0.000000
#> COSMIC_16 6.352880 11.781069 11.383645 18.382613 10.442240
#> COSMIC_17 0.000000 0.000000 0.138013 1642.620944 0.000000
#> COSMIC_18 10389.077591 336.244681 0.000000 824.282503 3089.548636
#> COSMIC_19 8.116437 0.000000 0.000000 2.757814 0.000000
#> COSMIC_20 0.268375 0.000000 2.720388 5.982007 0.000000
#> COSMIC_21 0.000000 0.000000 0.000000 0.000000 6.680742
#> COSMIC_22 5.430861 0.000000 0.000000 4.857105 0.000000
#> COSMIC_23 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_24 0.834280 0.000000 1.417995 2.584883 0.000000
#> COSMIC_25 0.000000 4.803570 0.000000 0.000000 0.000000
#> COSMIC_26 5.146132 0.000000 3.721977 8.602417 0.345477
#> COSMIC_27 0.818058 0.619339 0.761797 0.000000 0.000000
#> COSMIC_28 0.000000 2.255656 0.000000 0.000000 34.627985
#> COSMIC_29 0.000000 0.000000 0.000000 0.000000 0.426970
#> COSMIC_30 14.907068 0.000000 4.971933 13.449397 0.000000
#> Sample_17 Sample_18 Sample_19 Sample_20 Sample_21
#> COSMIC_1 8316.462448 449.235151 4386.555077 363.844840 2.290543
#> COSMIC_2 2279.911970 188.412956 0.000000 0.976010 0.000000
#> COSMIC_3 0.000000 0.000000 10.619926 0.000000 4153.467439
#> COSMIC_4 0.000000 0.000000 0.000000 0.000000 2.701635
#> COSMIC_5 0.000000 0.000000 10084.344976 269.259689 658.647006
#> COSMIC_6 5025.247765 0.000000 0.000000 0.000000 678.815968
#> COSMIC_7 0.747681 0.000000 0.000000 0.000000 0.000000
#> COSMIC_8 0.000000 2273.138539 14.053514 0.000000 4977.312139
#> COSMIC_9 0.000000 0.000000 0.000000 2.240584 0.000000
#> COSMIC_10 0.000000 0.744366 0.000000 0.546513 2.916468
#> COSMIC_11 0.000000 0.000000 3.265850 0.000000 0.000000
#> COSMIC_12 10187.187402 0.000000 7976.495356 894.404021 0.000000
#> COSMIC_13 0.554193 611.961539 2670.903273 0.000000 2783.340620
#> COSMIC_14 0.000000 0.130862 0.843056 0.000000 0.000000
#> COSMIC_15 2.799945 0.000000 1.940155 0.000000 2.830738
#> COSMIC_16 0.000000 0.000000 0.000000 4.445176 0.000000
#> COSMIC_17 1856.568846 2002.188974 0.000000 171.786377 0.000000
#> COSMIC_18 0.422052 0.000000 7727.188645 864.379911 0.000000
#> COSMIC_19 0.000000 0.000000 5.532711 0.000000 7.724353
#> COSMIC_20 0.000000 0.000000 0.000000 2.817051 0.000000
#> COSMIC_21 2.655370 0.000000 0.000000 3.740846 0.000000
#> COSMIC_22 0.000000 0.000000 4.687859 1.469317 0.000000
#> COSMIC_23 0.000000 0.000000 0.000000 1.620364 0.000000
#> COSMIC_24 0.442328 0.000000 1.042670 0.000000 0.264848
#> COSMIC_25 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_26 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_27 0.000000 0.000000 0.000000 0.186345 0.868987
#> COSMIC_28 0.000000 41.821921 0.000000 11.010071 50.943245
#> COSMIC_29 0.000000 4.365692 0.000000 3.883271 9.876013
#> COSMIC_30 0.000000 0.000000 4.526931 0.389614 0.000000
#> Sample_22 Sample_23 Sample_24 Sample_25 Sample_26
#> COSMIC_1 6540.916420 6.159738 0.055064 1452.748133 1094.123285
#> COSMIC_2 0.000000 0.000000 0.000000 1077.063506 0.025763
#> COSMIC_3 9515.382232 5.609259 9861.205426 0.000000 0.000000
#> COSMIC_4 5.436190 0.000000 1.031979 0.000000 0.000000
#> COSMIC_5 19242.733385 716.821835 18259.774984 0.000000 0.000000
#> COSMIC_6 2303.560317 590.443877 0.000000 1077.149896 2593.375058
#> COSMIC_7 0.000000 0.000000 0.547807 0.000000 0.000000
#> COSMIC_8 649.560645 397.525523 1011.946226 0.000000 1027.564189
#> COSMIC_9 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_10 4.076000 0.000000 0.000000 0.000000 0.600252
#> COSMIC_11 0.000000 0.366592 0.032034 0.000000 0.000000
#> COSMIC_12 0.000000 11.509237 0.000000 0.000000 0.000000
#> COSMIC_13 2.206680 0.000000 11882.297110 0.000000 629.765176
#> COSMIC_14 1.424192 0.000000 0.000000 4.153187 0.000000
#> COSMIC_15 0.000000 2.597857 0.008799 5.873210 0.000000
#> COSMIC_16 0.000000 0.480866 0.000000 0.000000 0.000000
#> COSMIC_17 0.000000 715.327401 0.000000 2647.566963 586.764687
#> COSMIC_18 0.000000 1952.671547 4876.507688 3890.903392 0.615152
#> COSMIC_19 2.685663 3.146145 1.567203 0.000000 0.000000
#> COSMIC_20 0.000000 3.430529 0.000000 6.541714 0.000000
#> COSMIC_21 0.000000 0.000000 0.000000 0.000000 1.270163
#> COSMIC_22 0.000000 2.222490 0.000000 0.000000 0.000000
#> COSMIC_23 4.809075 0.000000 0.000000 0.000000 0.000000
#> COSMIC_24 0.000000 3.288456 0.000000 0.000000 0.000000
#> COSMIC_25 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_26 0.000000 0.398648 0.115265 0.000000 0.000000
#> COSMIC_27 0.000000 0.000000 0.000000 0.000000 0.000000
#> COSMIC_28 77.893251 0.000000 0.000000 0.000000 9.215891
#> COSMIC_29 6.315948 0.000000 0.000000 0.000000 1.680384
#> COSMIC_30 0.000000 0.000000 0.910415 0.000000 0.000000
#> Sample_27 Sample_28 Sample_29 Sample_30
#> COSMIC_1 0.000000 0.500188 607.006162 3.733558
#> COSMIC_2 0.000000 0.000000 0.000000 0.000000
#> COSMIC_3 17.937813 201.260807 165.569996 0.000000
#> COSMIC_4 2.513001 2.925134 6.355168 0.000000
#> COSMIC_5 1491.103136 1189.447225 0.000000 0.000000
#> COSMIC_6 3.892577 0.000000 0.000000 673.361426
#> COSMIC_7 0.000000 0.000000 0.000000 0.724157
#> COSMIC_8 2179.372379 0.000000 960.287135 881.374297
#> COSMIC_9 1.022470 0.000000 0.000000 3.264570
#> COSMIC_10 1.467921 0.999990 0.000000 0.981160
#> COSMIC_11 0.000000 0.000000 0.062670 0.000000
#> COSMIC_12 2830.082067 356.938310 844.711035 1000.685511
#> COSMIC_13 2910.433262 1.442665 3.363711 0.000000
#> COSMIC_14 0.000000 0.000000 0.000000 0.000000
#> COSMIC_15 0.000000 0.000000 0.000000 0.000000
#> COSMIC_16 7.868604 8.495648 0.000000 0.000000
#> COSMIC_17 0.065766 0.000000 1048.224909 341.855428
#> COSMIC_18 639.739510 1192.979715 0.000000 0.392853
#> COSMIC_19 0.000000 0.000000 2.545339 1.095533
#> COSMIC_20 0.000000 0.438308 2.757058 0.000000
#> COSMIC_21 0.439556 3.331728 2.698298 0.060492
#> COSMIC_22 0.000000 0.000000 0.372904 0.000000
#> COSMIC_23 0.000000 0.000000 0.000000 0.000000
#> COSMIC_24 0.000000 2.817830 0.935905 0.000000
#> COSMIC_25 3.769250 0.000000 0.000000 3.310930
#> COSMIC_26 0.000000 2.716184 0.000000 0.000000
#> COSMIC_27 0.292688 0.475940 0.000000 0.000000
#> COSMIC_28 0.000000 8.230327 0.000000 8.160085
#> COSMIC_29 0.000000 0.000000 0.000000 0.000000
#> COSMIC_30 0.000000 0.000000 3.109709 0.000000
# Check ?sig_fit for sig_db options
# e.g., use the COSMIC SBS v3
sig_fit(data, sig_index = "ALL", sig_db = "SBS")
#> ℹ [2024-08-04 14:44:52.792202]: Started.
#> ✔ [2024-08-04 14:44:52.793705]: Signature index detected.
#> ℹ [2024-08-04 14:44:52.795076]: Checking signature database in package.
#> ℹ [2024-08-04 14:44:52.798386]: Checking signature index.
#> ℹ [2024-08-04 14:44:52.799865]: Valid index for db 'SBS':
#> 1 2 3 4 5 6 7a 7b 7c 7d 8 9 10a 10b 11 12 13 14 15 16 17a 17b 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 84 85 86 87 88 89 90
#> ✔ [2024-08-04 14:44:52.80159]: Database and index checked.
#> ✔ [2024-08-04 14:44:52.803625]: Signature normalized.
#> ℹ [2024-08-04 14:44:52.805068]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:52.806484]: Checked.
#> ℹ [2024-08-04 14:44:52.807817]: Checking rownames for catalog matrix and signature matrix.
#> ℹ [2024-08-04 14:44:52.809186]: Matrix V and W don't have same orders. Try reordering...
#> ✔ [2024-08-04 14:44:52.81069]: Checked.
#> ✔ [2024-08-04 14:44:52.812097]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:52.813494]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:52.814839]: Calling function.
#> ℹ [2024-08-04 14:44:52.816531]: Fitting sample: Sample_1
#> ℹ [2024-08-04 14:44:52.819893]: Fitting sample: Sample_2
#> ℹ [2024-08-04 14:44:52.823678]: Fitting sample: Sample_3
#> ℹ [2024-08-04 14:44:52.827028]: Fitting sample: Sample_4
#> ℹ [2024-08-04 14:44:52.830553]: Fitting sample: Sample_5
#> ℹ [2024-08-04 14:44:52.834314]: Fitting sample: Sample_6
#> ℹ [2024-08-04 14:44:52.837776]: Fitting sample: Sample_7
#> ℹ [2024-08-04 14:44:52.841288]: Fitting sample: Sample_8
#> ℹ [2024-08-04 14:44:52.844759]: Fitting sample: Sample_9
#> ℹ [2024-08-04 14:44:52.848353]: Fitting sample: Sample_10
#> ℹ [2024-08-04 14:44:52.851695]: Fitting sample: Sample_11
#> ℹ [2024-08-04 14:44:52.855032]: Fitting sample: Sample_12
#> ℹ [2024-08-04 14:44:52.858595]: Fitting sample: Sample_13
#> ℹ [2024-08-04 14:44:52.862153]: Fitting sample: Sample_14
#> ℹ [2024-08-04 14:44:52.86558]: Fitting sample: Sample_15
#> ℹ [2024-08-04 14:44:52.868911]: Fitting sample: Sample_16
#> ℹ [2024-08-04 14:44:52.872537]: Fitting sample: Sample_17
#> ℹ [2024-08-04 14:44:52.876085]: Fitting sample: Sample_18
#> ℹ [2024-08-04 14:44:52.879736]: Fitting sample: Sample_19
#> ℹ [2024-08-04 14:44:52.883405]: Fitting sample: Sample_20
#> ℹ [2024-08-04 14:44:52.8871]: Fitting sample: Sample_21
#> ℹ [2024-08-04 14:44:52.890651]: Fitting sample: Sample_22
#> ℹ [2024-08-04 14:44:52.893972]: Fitting sample: Sample_23
#> ℹ [2024-08-04 14:44:52.897363]: Fitting sample: Sample_24
#> ℹ [2024-08-04 14:44:52.900674]: Fitting sample: Sample_25
#> ℹ [2024-08-04 14:44:52.904116]: Fitting sample: Sample_26
#> ℹ [2024-08-04 14:44:52.907596]: Fitting sample: Sample_27
#> ℹ [2024-08-04 14:44:52.911031]: Fitting sample: Sample_28
#> ℹ [2024-08-04 14:44:52.91458]: Fitting sample: Sample_29
#> ℹ [2024-08-04 14:44:52.918061]: Fitting sample: Sample_30
#> ✔ [2024-08-04 14:44:52.921463]: Done.
#> ℹ [2024-08-04 14:44:52.923605]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:52.926977]: Done.
#> ℹ [2024-08-04 14:44:52.929136]: 0.137 secs elapsed.
#> Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6
#> SBS1 446.06618 352.314782 168.179569 0.000000 5.994249 25.885569
#> SBS2 0.00000 3425.967684 416.028733 640.708332 910.549175 344.154284
#> SBS3 3771.33903 0.000000 529.937946 846.042672 0.000000 73.000551
#> SBS4 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS5 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS6 0.00000 1726.029066 2043.106593 0.000000 0.000000 204.770660
#> SBS7a 80.53353 31.357883 96.283573 0.000000 14.013953 9.759239
#> SBS7b 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS7c 0.00000 0.000000 9.552791 13.184604 0.000000 0.000000
#> SBS7d 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS8 10694.42205 3007.207116 241.938865 523.427765 0.000000 186.857134
#> SBS9 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS10a 153.11952 1.416355 0.000000 0.000000 0.000000 0.000000
#> SBS10b 0.00000 0.000000 0.000000 0.000000 0.000000 9.750629
#> SBS11 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS12 6574.02430 1225.580812 802.817948 1287.869219 0.000000 6.894609
#> SBS13 0.00000 4656.694903 2134.082718 3156.021470 1048.843041 67.457769
#> SBS14 28.40582 205.282129 141.193981 0.000000 0.000000 14.360009
#> SBS15 0.00000 243.401641 285.680515 85.001522 0.492277 10.182468
#> SBS16 0.00000 26.701935 156.635587 28.033701 0.000000 16.904165
#> SBS17a 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS17b 633.73405 89.498911 88.722111 55.729454 5.409310 4.165818
#> SBS18 759.74051 0.000000 538.012825 685.037228 483.659079 308.830495
#> SBS19 992.13906 332.607459 132.973567 197.661357 13.525765 16.975074
#> SBS20 0.00000 542.428688 538.347687 60.203392 0.000000 55.499404
#> SBS21 674.43422 227.167678 141.056290 149.539709 0.000000 6.656367
#> SBS22 0.00000 0.000000 116.105848 85.886136 5.663501 0.000000
#> SBS23 0.00000 0.000000 78.592222 0.000000 0.000000 0.000000
#> SBS24 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS25 0.00000 0.000000 0.000000 0.000000 4.577926 9.073294
#> SBS26 1368.51363 675.253249 311.575696 432.320720 0.000000 0.000000
#> SBS27 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS28 0.00000 11.237706 51.069161 1.403327 4.411267 10.817382
#> SBS29 0.00000 103.345568 260.388505 176.475073 23.588253 5.965772
#> SBS30 28.26495 133.174428 60.370199 274.593445 13.364214 0.045889
#> SBS31 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS32 582.70432 0.000000 0.000000 0.000000 0.000000 7.419328
#> SBS33 74.60755 0.000000 0.000000 11.095022 0.000000 0.000000
#> SBS34 163.81922 32.572782 38.025511 2.880772 0.000000 0.000000
#> SBS35 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS36 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS37 45.71330 0.000000 43.451880 0.000000 0.000000 0.000000
#> SBS38 95.69621 27.303541 0.000000 0.000000 28.717133 5.517314
#> SBS39 4669.90834 413.444300 495.025206 981.152408 37.940224 98.709340
#> SBS40 4839.36935 0.000000 0.000000 0.000000 0.000000 16.563255
#> SBS41 402.41959 306.407425 0.000000 139.922437 0.000000 0.000000
#> SBS42 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS43 476.83270 89.510008 33.200380 93.713704 7.627752 12.787340
#> SBS44 800.69479 0.000000 0.000000 30.143590 0.000000 0.000000
#> SBS45 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS46 2667.89235 472.188567 206.830069 343.326092 25.375581 20.077460
#> SBS47 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS48 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS49 0.00000 12.251611 42.858293 0.000000 0.000000 4.059684
#> SBS50 143.97597 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS51 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS52 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS53 0.00000 45.504335 4.587349 87.644537 8.234425 0.000000
#> SBS54 464.72114 333.495978 412.021703 149.746217 0.000000 29.980835
#> SBS55 128.38732 0.000000 17.731337 0.000000 0.000000 6.235518
#> SBS56 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS57 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS58 334.00510 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS59 0.00000 0.000000 26.671728 47.236094 22.587013 3.198901
#> SBS60 0.00000 0.000000 0.000000 0.000000 2.440548 0.000000
#> SBS84 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS85 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS86 0.00000 74.653461 41.588576 0.000000 25.721078 16.886622
#> SBS87 0.00000 0.000000 63.557111 0.000000 0.000000 3.557824
#> SBS88 0.00000 0.000000 1.797925 0.000000 2.264237 0.000000
#> SBS89 618.90584 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS90 45.61003 0.000000 0.000000 0.000000 0.000000 0.000000
#> Sample_7 Sample_8 Sample_9 Sample_10 Sample_11 Sample_12
#> SBS1 22.282475 537.811662 111.823576 158.293396 454.206109 0.00000
#> SBS2 71.991947 183.018549 157.000784 947.247238 566.548529 805.65037
#> SBS3 0.000000 143.899490 0.000000 0.000000 0.000000 6184.00074
#> SBS4 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS5 0.000000 0.000000 0.000000 903.074564 0.000000 0.00000
#> SBS6 134.862279 44.825275 54.854165 0.000000 534.236805 0.00000
#> SBS7a 12.390872 0.000000 69.774383 55.049491 46.277416 159.64607
#> SBS7b 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS7c 0.000000 0.000000 18.597067 0.000000 0.000000 8.01225
#> SBS7d 0.000000 11.646995 24.273000 0.000000 5.394268 0.00000
#> SBS8 0.000000 46.345664 752.023973 1726.187855 182.572187 3085.33988
#> SBS9 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS10a 0.000000 0.000000 0.000000 25.722906 0.000000 0.00000
#> SBS10b 0.000000 64.443724 85.060103 2.968258 41.641692 0.00000
#> SBS11 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS12 20.024290 40.777575 0.000000 313.261304 304.806769 6665.67297
#> SBS13 342.294209 36.903526 618.547019 123.896219 709.031907 3698.10516
#> SBS14 0.000000 0.000000 6.393714 32.313379 56.934479 0.00000
#> SBS15 27.412567 0.000000 0.000000 0.000000 14.409081 0.00000
#> SBS16 21.376273 49.207382 43.774168 165.034005 166.120986 200.88922
#> SBS17a 30.455635 0.000000 822.375525 2.517252 0.000000 0.00000
#> SBS17b 83.545702 2.816105 1995.236792 50.873045 41.974652 272.36890
#> SBS18 422.824481 602.084768 59.882419 1358.752476 19.009159 11057.12324
#> SBS19 12.408097 48.015048 172.717375 169.932277 118.193294 970.86051
#> SBS20 50.695857 0.000000 0.000000 0.000000 46.093320 0.00000
#> SBS21 8.783053 26.942837 0.000000 0.000000 51.083282 745.05904
#> SBS22 11.882019 2.636566 0.000000 19.390117 59.053621 490.51076
#> SBS23 3.688235 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS24 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS25 30.355093 0.000000 257.444434 326.561438 77.093342 0.00000
#> SBS26 27.409536 0.000000 0.000000 0.000000 10.841186 923.79026
#> SBS27 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS28 0.000000 0.000000 0.000000 0.000000 0.000000 14.44337
#> SBS29 27.575693 46.107948 0.000000 0.000000 118.269963 509.55429
#> SBS30 13.698437 128.585141 455.947345 108.207348 230.267852 1008.02779
#> SBS31 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS32 0.000000 0.000000 0.000000 110.800641 0.000000 0.00000
#> SBS33 0.000000 1.878902 3.327825 0.000000 0.000000 33.75485
#> SBS34 0.000000 0.921931 0.000000 52.744061 33.554375 0.00000
#> SBS35 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS36 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS37 0.139980 0.000000 346.544066 80.444489 87.335575 423.62339
#> SBS38 2.881911 0.000000 0.000000 0.000000 0.000000 44.98554
#> SBS39 98.537850 46.354419 1171.321287 961.678364 274.919586 6302.87792
#> SBS40 0.000000 82.379062 52.899760 1069.312766 432.680915 1611.84753
#> SBS41 0.000000 0.000000 46.316697 0.000000 0.000000 0.00000
#> SBS42 0.000000 51.687712 0.000000 0.000000 70.503752 0.00000
#> SBS43 6.868222 10.215896 99.515868 0.000000 0.000000 586.08394
#> SBS44 0.000000 38.032543 0.000000 148.834240 76.628999 709.29531
#> SBS45 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS46 32.187431 42.702520 344.814521 326.281258 131.710817 1719.69606
#> SBS47 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS48 0.000000 2.696820 0.000000 3.243888 0.427387 0.00000
#> SBS49 4.502460 0.000000 0.000000 0.000000 4.302329 0.00000
#> SBS50 0.000000 0.000000 5.589561 57.802376 0.000000 0.00000
#> SBS51 0.000000 12.081070 0.000000 0.000000 0.000000 0.00000
#> SBS52 0.000000 0.172794 0.000000 0.000000 0.000000 0.00000
#> SBS53 10.365112 6.245482 0.000000 0.000000 0.000000 408.17094
#> SBS54 34.031074 19.374629 193.897934 26.152249 144.294493 899.65197
#> SBS55 4.295673 6.462695 61.642802 84.973562 26.553492 220.06937
#> SBS56 0.000000 0.000000 0.000000 2.141215 20.306141 0.00000
#> SBS57 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS58 0.000000 0.000000 38.156071 0.000000 0.000000 0.00000
#> SBS59 15.640245 0.000000 24.927538 16.528503 0.000000 208.88834
#> SBS60 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS84 0.000000 9.483127 0.000000 7.077683 45.488530 0.00000
#> SBS85 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS86 0.000000 28.019974 0.000000 67.590799 53.233710 0.00000
#> SBS87 7.991066 17.222170 29.320231 0.000000 0.000000 0.00000
#> SBS88 3.602225 0.000000 0.000000 40.716475 0.000000 0.00000
#> SBS89 0.000000 0.000000 0.000000 167.394862 0.000000 0.00000
#> SBS90 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
#> Sample_13 Sample_14 Sample_15 Sample_16 Sample_17 Sample_18
#> SBS1 28.001829 32.192936 306.827718 0.000000 3768.83346 339.680283
#> SBS2 134.544443 988.792807 550.127522 163.748275 1763.48657 293.046081
#> SBS3 27.754255 59.724612 0.000000 870.820214 0.00000 0.000000
#> SBS4 0.000000 0.000000 0.000000 0.000000 549.77782 0.000000
#> SBS5 0.000000 0.000000 174.813970 0.000000 0.00000 0.000000
#> SBS6 7.846333 135.073945 191.795767 0.000000 3912.75669 0.000000
#> SBS7a 0.000000 31.443795 78.993069 19.321636 147.51575 2.606657
#> SBS7b 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS7c 3.931945 0.550038 28.913647 3.962225 34.41563 19.927144
#> SBS7d 0.000000 0.000000 3.740986 0.000000 0.00000 15.357364
#> SBS8 271.669355 194.303767 413.159576 104.067645 1313.15753 1426.620135
#> SBS9 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS10a 0.000000 0.000000 0.000000 0.000000 0.00000 14.075468
#> SBS10b 0.000000 5.034643 0.000000 0.000000 497.14044 66.038580
#> SBS11 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS12 199.802691 529.670206 386.074220 876.799245 4260.22235 0.000000
#> SBS13 636.096640 876.428834 2796.783863 611.170635 305.12018 569.672029
#> SBS14 0.000000 16.249060 41.575151 0.000000 0.00000 35.332573
#> SBS15 29.754648 3.102191 33.512358 0.000000 0.00000 0.000000
#> SBS16 0.000000 46.548339 249.448229 5.676878 0.00000 24.323727
#> SBS17a 0.000000 0.000000 302.834378 0.000000 129.11193 411.929867
#> SBS17b 5.531471 26.832580 850.430656 14.949794 1035.22385 974.709046
#> SBS18 315.312203 25.944850 847.661354 3170.336034 0.00000 178.789240
#> SBS19 32.444005 122.880074 207.207897 108.293262 969.02642 103.898398
#> SBS20 34.678629 4.941801 0.000000 0.000000 748.15868 0.000000
#> SBS21 34.167632 58.567700 34.163499 119.366888 809.51047 0.000000
#> SBS22 6.136127 41.278138 93.139137 80.829564 0.00000 0.000000
#> SBS23 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS24 0.000000 26.573935 0.000000 0.000000 270.11766 0.000000
#> SBS25 0.000000 0.000000 296.198796 0.000000 0.00000 15.144629
#> SBS26 84.243212 171.407581 92.291742 173.750835 1536.70282 0.000000
#> SBS27 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS28 0.000000 0.000000 0.000000 21.147276 0.00000 0.000000
#> SBS29 18.912710 15.244739 182.196469 108.856508 26.00825 0.000000
#> SBS30 10.798087 140.607690 503.657207 25.596949 788.99021 168.616351
#> SBS31 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS32 0.000000 0.000000 0.000000 0.000000 0.00000 84.655713
#> SBS33 0.000000 5.713271 0.000000 0.000000 85.73891 0.000000
#> SBS34 2.189698 7.599702 43.804497 0.000000 102.82132 36.485559
#> SBS35 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS36 0.000000 0.000000 0.000000 0.000000 259.24275 0.000000
#> SBS37 0.000000 25.197289 288.315048 0.000000 0.00000 160.147632
#> SBS38 9.332443 0.000000 0.000000 75.290621 0.00000 0.000000
#> SBS39 68.781644 144.015309 980.349565 607.706490 0.00000 216.281382
#> SBS40 0.000000 64.039981 0.000000 0.000000 870.76706 0.000000
#> SBS41 21.796491 40.795855 22.260438 0.000000 0.00000 20.375135
#> SBS42 0.000000 0.000000 0.000000 0.000000 321.62150 0.000000
#> SBS43 13.152285 12.929337 0.000000 104.533541 123.42461 28.622352
#> SBS44 0.000000 77.360275 0.000000 0.000000 130.97719 0.000000
#> SBS45 0.000000 0.000000 0.000000 0.000000 61.07298 0.000000
#> SBS46 61.389024 156.897641 396.162303 200.076291 1852.04462 165.417732
#> SBS47 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS48 0.000000 0.000000 0.000000 0.000000 25.90892 0.000000
#> SBS49 0.000000 2.525869 0.000000 10.346805 17.46214 0.000000
#> SBS50 0.000000 0.000000 0.000000 0.000000 0.00000 37.419504
#> SBS51 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS52 0.000000 0.000000 0.000000 0.000000 11.00697 0.000000
#> SBS53 17.890481 7.681697 11.629275 58.806127 0.00000 0.000000
#> SBS54 28.447591 76.502615 210.877981 118.741754 816.36626 71.480806
#> SBS55 0.000000 0.000000 57.589435 7.764625 0.00000 23.857029
#> SBS56 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS57 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS58 0.000000 0.000000 0.000000 0.000000 0.00000 13.990064
#> SBS59 12.394129 0.000000 35.175459 64.039886 0.00000 0.000000
#> SBS60 0.000000 0.000000 1.156692 0.000000 0.00000 0.000000
#> SBS84 0.000000 0.000000 55.998385 0.000000 0.00000 0.000000
#> SBS85 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000
#> SBS86 0.000000 36.346898 0.000000 0.000000 91.49678 0.000000
#> SBS87 0.000000 0.000000 0.000000 0.000000 37.77131 0.000000
#> SBS88 0.000000 0.000000 19.133710 0.000000 0.00000 37.766637
#> SBS89 0.000000 0.000000 0.000000 0.000000 0.00000 12.844511
#> SBS90 0.000000 0.000000 0.000000 0.000000 0.00000 2.888371
#> Sample_19 Sample_20 Sample_21 Sample_22 Sample_23 Sample_24
#> SBS1 2039.96413 149.158926 286.642351 3607.798297 64.813752 258.64970
#> SBS2 445.80008 13.538846 490.209770 0.000000 29.791716 1941.03529
#> SBS3 678.52730 169.659789 1068.273153 3921.433569 0.000000 3183.74145
#> SBS4 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS5 201.85371 0.000000 0.000000 4030.270929 12.474698 0.00000
#> SBS6 417.35098 25.618342 129.473906 1516.347817 302.044684 315.32997
#> SBS7a 133.10227 3.344145 0.000000 0.000000 14.830055 139.85363
#> SBS7b 0.00000 0.000000 0.000000 260.023779 49.090467 0.00000
#> SBS7c 25.69606 6.172160 0.000000 0.000000 0.000000 0.00000
#> SBS7d 52.27566 0.000000 0.000000 3.906008 14.841736 0.00000
#> SBS8 1040.78581 29.602216 3384.145192 3682.760308 167.949333 3361.33783
#> SBS9 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS10a 0.00000 0.000000 7.837407 0.000000 0.000000 0.00000
#> SBS10b 120.25710 19.063797 0.000000 215.971775 4.815127 0.00000
#> SBS11 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS12 4681.57550 377.313258 22.330920 1826.753963 26.915648 2263.77573
#> SBS13 2149.95080 0.000000 2443.237730 0.000000 0.000000 10264.02086
#> SBS14 0.00000 0.000000 198.887944 95.039818 0.000000 247.25276
#> SBS15 0.00000 0.000000 118.877164 0.000000 33.665517 240.66544
#> SBS16 549.16383 1.970066 120.545561 912.347449 80.202308 992.92106
#> SBS17a 0.00000 13.180932 9.827664 0.000000 144.120515 0.00000
#> SBS17b 202.08236 91.997549 69.766747 367.148242 351.623623 343.39896
#> SBS18 8697.20643 932.812046 198.986888 408.409474 2102.526390 5241.52426
#> SBS19 968.68842 75.833193 131.918504 714.956053 32.960581 622.83147
#> SBS20 0.00000 2.976527 0.000000 0.000000 107.462006 0.00000
#> SBS21 576.84560 47.030647 0.000000 203.966450 26.326930 49.51724
#> SBS22 502.35846 32.686480 0.000000 530.214364 39.459208 491.53506
#> SBS23 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS24 0.00000 0.000000 0.000000 345.054470 0.000000 0.00000
#> SBS25 0.00000 0.000000 0.000000 0.000000 81.637871 428.00593
#> SBS26 1314.17646 182.324101 0.000000 0.000000 14.955289 0.00000
#> SBS27 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS28 0.00000 0.000000 17.709407 196.736072 0.000000 85.54777
#> SBS29 697.36208 61.226818 0.000000 79.651009 65.803910 620.90145
#> SBS30 1308.97875 72.536829 27.856473 1672.430828 0.000000 1850.79197
#> SBS31 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS32 0.00000 0.000000 168.914809 0.000000 28.444934 0.00000
#> SBS33 34.21223 4.326822 0.000000 0.000000 0.000000 0.00000
#> SBS34 89.32408 0.000000 44.871504 239.198619 0.000000 136.04087
#> SBS35 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS36 0.00000 0.000000 0.000000 970.050452 0.000000 0.00000
#> SBS37 243.31956 0.000000 94.901735 1355.740141 53.064000 997.58414
#> SBS38 0.00000 0.000000 15.619834 0.000000 20.502614 0.00000
#> SBS39 2033.14621 2.492142 1795.540572 4557.112712 163.341544 6684.12750
#> SBS40 507.37936 0.000000 698.355023 921.745663 0.000000 631.20712
#> SBS41 0.00000 0.000000 214.408512 0.000000 0.000000 165.81377
#> SBS42 387.17367 1.843926 0.000000 215.393710 0.000000 0.00000
#> SBS43 77.22160 19.283081 81.674594 0.000000 38.458833 17.81008
#> SBS44 334.40110 0.000000 327.136899 1428.965561 0.000000 196.31151
#> SBS45 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS46 1187.63294 149.120705 374.743621 1243.993328 82.355773 1204.33307
#> SBS47 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS48 17.09584 3.043544 0.000000 42.086791 3.255971 0.00000
#> SBS49 20.54985 2.861795 0.000000 0.000000 12.742081 0.00000
#> SBS50 0.00000 0.000000 74.725290 285.809203 0.000000 0.00000
#> SBS51 0.00000 0.000000 0.000000 177.941426 0.000000 0.00000
#> SBS52 0.00000 0.000000 0.000000 13.832885 0.000000 0.00000
#> SBS53 245.01094 30.934044 0.000000 0.000000 30.052391 70.33150
#> SBS54 680.59053 43.892390 63.077704 775.743274 112.637111 777.30314
#> SBS55 133.63464 0.000000 65.723138 399.837615 19.689125 404.77848
#> SBS56 0.00000 0.000000 0.000000 75.157938 0.000000 0.00000
#> SBS57 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS58 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS59 61.18227 8.445741 0.221444 0.000000 40.352963 163.47821
#> SBS60 0.00000 0.000000 0.000000 0.000000 0.000000 10.53115
#> SBS84 13.79664 0.000000 0.000000 862.070844 0.000000 522.16438
#> SBS85 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> SBS86 0.00000 0.000000 16.304181 201.099164 0.000000 92.05212
#> SBS87 22.32674 22.709145 0.000000 0.000000 38.791296 0.00000
#> SBS88 0.00000 0.000000 142.860995 0.000000 0.000000 341.17166
#> SBS89 0.00000 0.000000 426.393365 0.000000 0.000000 538.32346
#> SBS90 0.00000 0.000000 0.000000 0.000000 0.000000 0.00000
#> Sample_25 Sample_26 Sample_27 Sample_28 Sample_29 Sample_30
#> SBS1 715.26298 634.542555 97.144930 17.132813 331.946933 78.026773
#> SBS2 915.44808 117.860979 522.154264 0.000000 12.821998 5.844568
#> SBS3 0.00000 135.332768 98.776505 128.519753 0.000000 0.000000
#> SBS4 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS5 0.00000 0.000000 0.000000 161.996986 0.000000 0.000000
#> SBS6 689.16873 1541.241453 0.000000 0.000000 3.783462 383.761328
#> SBS7a 41.41883 38.677954 0.000000 11.908640 20.280163 16.964497
#> SBS7b 99.59051 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS7c 0.00000 0.000000 6.486657 0.000000 8.811085 3.691475
#> SBS7d 34.15372 2.395097 0.000000 3.955165 9.851980 0.000000
#> SBS8 0.00000 681.108432 1719.614316 71.572480 806.281840 662.859786
#> SBS9 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS10a 0.00000 11.579627 0.000000 0.000000 3.388724 11.896212
#> SBS10b 118.53761 72.047259 0.000000 0.000000 48.151659 9.716146
#> SBS11 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS12 0.00000 0.000000 1331.874170 256.765098 385.215644 384.698087
#> SBS13 142.54453 549.553092 2521.993959 0.000000 3.829160 0.000000
#> SBS14 0.00000 89.353574 3.976861 0.000000 0.000000 0.000000
#> SBS15 0.00000 164.337312 45.066962 0.000000 0.000000 28.937012
#> SBS16 47.89028 49.917611 54.130287 59.299428 0.000000 0.000000
#> SBS17a 527.28234 109.877255 0.000000 0.000000 193.647345 49.848785
#> SBS17b 1249.35844 316.036119 56.818127 17.498466 513.666816 184.072296
#> SBS18 4092.66460 0.000000 719.675872 1323.070156 115.834518 59.643639
#> SBS19 102.12862 57.870410 247.806564 56.428808 118.162708 79.374590
#> SBS20 139.14226 418.962491 48.086652 10.474487 0.000000 134.360464
#> SBS21 54.80644 84.178097 141.601596 33.725442 44.775909 67.720297
#> SBS22 0.00000 0.000000 18.652217 65.052251 0.000000 0.000000
#> SBS23 0.00000 26.746002 0.000000 0.000000 0.000000 0.000000
#> SBS24 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS25 123.31873 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS26 0.00000 57.640211 563.624099 56.823231 92.462481 157.644444
#> SBS27 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS28 0.00000 22.171820 0.000000 6.174538 0.000000 4.644259
#> SBS29 109.12476 107.511515 48.474971 51.301875 0.000000 0.000000
#> SBS30 112.84759 0.000000 228.071677 83.378787 145.874416 0.000000
#> SBS31 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS32 0.00000 4.184894 0.000000 5.789955 35.307072 35.069669
#> SBS33 0.00000 0.000000 8.064016 0.000000 5.887511 0.000000
#> SBS34 0.00000 19.802653 39.593289 0.000000 18.082041 11.071147
#> SBS35 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS36 0.00000 0.000000 0.000000 0.000000 18.240594 0.000000
#> SBS37 0.00000 16.316036 19.850480 60.193346 57.875193 28.620718
#> SBS38 71.42720 0.000000 15.461803 0.000000 0.000000 0.000000
#> SBS39 0.00000 0.000000 585.025564 219.133568 196.540684 56.636237
#> SBS40 0.00000 147.034337 0.000000 0.000000 0.000000 96.191112
#> SBS41 0.00000 0.000000 156.209343 0.000000 0.000000 25.061704
#> SBS42 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS43 116.79137 35.157954 44.196808 4.243583 41.828618 26.257371
#> SBS44 0.00000 0.000000 78.587032 0.000000 53.753195 0.000000
#> SBS45 0.00000 0.000000 0.000000 0.000000 0.000000 7.222362
#> SBS46 170.67822 94.349848 383.875257 90.990960 223.105675 180.740558
#> SBS47 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS48 10.63455 0.000000 0.000000 4.317328 1.643012 1.461703
#> SBS49 24.09664 18.294508 0.000000 2.687782 0.000000 3.089554
#> SBS50 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS51 0.00000 0.000000 0.000000 2.970443 0.000000 0.000000
#> SBS52 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS53 34.59448 0.000000 45.956342 33.204852 0.000000 2.130033
#> SBS54 205.88736 231.161914 116.190376 62.468310 69.307871 101.437669
#> SBS55 0.00000 3.962804 0.000000 26.370852 0.000000 0.000000
#> SBS56 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS57 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS58 0.00000 0.000000 0.000000 0.000000 54.231690 15.996187
#> SBS59 78.94552 0.000000 26.476898 18.953207 0.000000 3.123757
#> SBS60 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS84 0.00000 0.000000 0.000000 21.867725 0.000000 0.000000
#> SBS85 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000
#> SBS86 35.40706 34.931998 0.000000 0.000000 2.568502 0.000000
#> SBS87 98.84852 50.861422 0.000000 2.794004 7.374950 1.185562
#> SBS88 0.00000 0.000000 0.000000 1.935681 0.000000 0.000000
#> SBS89 0.00000 0.000000 96.482104 0.000000 0.000000 0.000000
#> SBS90 0.00000 0.000000 0.000000 0.000000 3.466548 0.000000
# Fitting with specified signatures
# opt 1. use selected reference signatures
sig_fit(data, sig_index = c(1, 5, 9, 2, 13), sig_db = "SBS")
#> ℹ [2024-08-04 14:44:52.937356]: Started.
#> ✔ [2024-08-04 14:44:52.939675]: Signature index detected.
#> ℹ [2024-08-04 14:44:52.941836]: Checking signature database in package.
#> ℹ [2024-08-04 14:44:52.946859]: Checking signature index.
#> ℹ [2024-08-04 14:44:52.949281]: Valid index for db 'SBS':
#> 1 2 3 4 5 6 7a 7b 7c 7d 8 9 10a 10b 11 12 13 14 15 16 17a 17b 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 84 85 86 87 88 89 90
#> ✔ [2024-08-04 14:44:52.951558]: Database and index checked.
#> ✔ [2024-08-04 14:44:52.953944]: Signature normalized.
#> ℹ [2024-08-04 14:44:52.956054]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:52.958142]: Checked.
#> ℹ [2024-08-04 14:44:52.960174]: Checking rownames for catalog matrix and signature matrix.
#> ℹ [2024-08-04 14:44:52.962236]: Matrix V and W don't have same orders. Try reordering...
#> ✔ [2024-08-04 14:44:52.964396]: Checked.
#> ✔ [2024-08-04 14:44:52.966454]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:52.968473]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:52.97054]: Calling function.
#> ℹ [2024-08-04 14:44:52.973019]: Fitting sample: Sample_1
#> ℹ [2024-08-04 14:44:52.975243]: Fitting sample: Sample_2
#> ℹ [2024-08-04 14:44:52.977415]: Fitting sample: Sample_3
#> ℹ [2024-08-04 14:44:52.979546]: Fitting sample: Sample_4
#> ℹ [2024-08-04 14:44:52.981683]: Fitting sample: Sample_5
#> ℹ [2024-08-04 14:44:52.983794]: Fitting sample: Sample_6
#> ℹ [2024-08-04 14:44:52.985927]: Fitting sample: Sample_7
#> ℹ [2024-08-04 14:44:52.988038]: Fitting sample: Sample_8
#> ℹ [2024-08-04 14:44:52.990175]: Fitting sample: Sample_9
#> ℹ [2024-08-04 14:44:52.992294]: Fitting sample: Sample_10
#> ℹ [2024-08-04 14:44:52.994452]: Fitting sample: Sample_11
#> ℹ [2024-08-04 14:44:52.996574]: Fitting sample: Sample_12
#> ℹ [2024-08-04 14:44:52.998715]: Fitting sample: Sample_13
#> ℹ [2024-08-04 14:44:53.000821]: Fitting sample: Sample_14
#> ℹ [2024-08-04 14:44:53.002985]: Fitting sample: Sample_15
#> ℹ [2024-08-04 14:44:53.005169]: Fitting sample: Sample_16
#> ℹ [2024-08-04 14:44:53.00735]: Fitting sample: Sample_17
#> ℹ [2024-08-04 14:44:53.00952]: Fitting sample: Sample_18
#> ℹ [2024-08-04 14:44:53.011661]: Fitting sample: Sample_19
#> ℹ [2024-08-04 14:44:53.01384]: Fitting sample: Sample_20
#> ℹ [2024-08-04 14:44:53.016013]: Fitting sample: Sample_21
#> ℹ [2024-08-04 14:44:53.018194]: Fitting sample: Sample_22
#> ℹ [2024-08-04 14:44:53.020355]: Fitting sample: Sample_23
#> ℹ [2024-08-04 14:44:53.022581]: Fitting sample: Sample_24
#> ℹ [2024-08-04 14:44:53.024775]: Fitting sample: Sample_25
#> ℹ [2024-08-04 14:44:53.027068]: Fitting sample: Sample_26
#> ℹ [2024-08-04 14:44:53.029295]: Fitting sample: Sample_27
#> ℹ [2024-08-04 14:44:53.031051]: Fitting sample: Sample_28
#> ℹ [2024-08-04 14:44:53.03253]: Fitting sample: Sample_29
#> ℹ [2024-08-04 14:44:53.034003]: Fitting sample: Sample_30
#> ✔ [2024-08-04 14:44:53.035446]: Done.
#> ℹ [2024-08-04 14:44:53.036796]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:53.039095]: Done.
#> ℹ [2024-08-04 14:44:53.040685]: 0.103 secs elapsed.
#> Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6 Sample_7
#> SBS1 0.0000 1115.5174 1181.6736 0.0000 27.23392 135.53666 111.05359
#> SBS5 34648.4926 9164.1835 6994.8599 5987.5245 515.60495 925.41428 752.16786
#> SBS9 7392.4247 714.1404 197.4413 812.2540 154.66961 123.51378 304.12381
#> SBS2 0.0000 3232.6125 289.5227 530.6185 916.24722 334.59501 66.95528
#> SBS13 719.0828 4597.5462 2106.5026 3255.6029 1081.24431 93.94027 362.69946
#> Sample_8 Sample_9 Sample_10 Sample_11 Sample_12 Sample_13 Sample_14
#> SBS1 587.99786 147.1861 162.0096 671.2564 0.0000 36.54608 47.55306
#> SBS5 1384.80775 1446.2158 6936.2449 3157.4381 38419.2774 1134.71898 2205.32076
#> SBS9 151.54187 5555.3650 1307.8428 128.8525 6490.2218 189.47990 129.34338
#> SBS2 195.57640 267.6864 941.5376 575.5768 219.4109 109.66959 969.59018
#> SBS13 72.07613 707.5467 365.3650 722.8763 4839.0899 646.58545 859.19262
#> Sample_15 Sample_16 Sample_17 Sample_18 Sample_19 Sample_20
#> SBS1 389.1707 4.650708 5234.915 343.9873 2130.8985 170.232187
#> SBS5 4320.0186 5663.703313 18611.358 1355.8435 24967.9758 1906.299465
#> SBS9 2615.9872 1186.572686 2250.317 2964.4311 3200.6463 513.459715
#> SBS2 586.5852 63.627029 1576.411 322.9761 194.9891 0.000000
#> SBS13 2876.2383 807.446263 0.000 584.7621 2397.4903 7.008633
#> Sample_21 Sample_22 Sample_23 Sample_24 Sample_25 Sample_26
#> SBS1 360.1966 4063.8892 301.202136 395.6656 1236.0071 1425.94080
#> SBS5 8066.6174 30202.4192 2611.606854 27744.4555 3755.3214 3251.66786
#> SBS9 1734.3629 3602.2796 1424.399907 4734.8930 3944.5535 681.38344
#> SBS2 370.9525 0.0000 7.180995 1730.8578 950.3892 78.28026
#> SBS13 2799.8706 488.4119 67.610108 11290.1281 275.7287 507.72764
#> Sample_27 Sample_28 Sample_29 Sample_30
#> SBS1 14.46626 39.49534 310.50110 230.3621
#> SBS5 6222.00235 2402.07223 1791.75036 2052.8025
#> SBS9 908.90204 480.48944 1525.63702 635.8353
#> SBS2 398.21552 0.00000 20.11152 0.0000
#> SBS13 2546.41383 50.94299 0.00000 0.0000
# opt 2. use user specified signatures
ref = get_sig_db()$db
ref[1:5, 1:5]
#> COSMIC_1 COSMIC_2 COSMIC_3 COSMIC_4 COSMIC_5
#> A[C>A]A 0.011098326 0.000682708 0.02217231 0.0365 0.014941548
#> A[C>A]C 0.009149341 0.000619107 0.01787168 0.0309 0.008960918
#> A[C>A]G 0.001490070 0.000099279 0.00213834 0.0183 0.002207846
#> A[C>A]T 0.006233885 0.000323891 0.01626515 0.0243 0.009206905
#> A[C>G]A 0.001801068 0.000263481 0.02400262 0.0097 0.011671022
ref = ref[, 1:10]
# The `sig` used here can be result object from `sig_extract`
# or any reference matrix with similar structure (96-motif)
v1 = sig_fit(data, sig = ref)
#> ℹ [2024-08-04 14:44:53.046826]: Started.
#> ℹ [2024-08-04 14:44:53.048593]: Signature index not detected.
#> ✔ [2024-08-04 14:44:53.050102]: Signature matrix/data.frame detected.
#> ✔ [2024-08-04 14:44:53.051504]: Database and index checked.
#> ✔ [2024-08-04 14:44:53.053025]: Signature normalized.
#> ℹ [2024-08-04 14:44:53.054404]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:53.055758]: Checked.
#> ℹ [2024-08-04 14:44:53.05711]: Checking rownames for catalog matrix and signature matrix.
#> ℹ [2024-08-04 14:44:53.058516]: Matrix V and W don't have same orders. Try reordering...
#> ✔ [2024-08-04 14:44:53.059984]: Checked.
#> ✔ [2024-08-04 14:44:53.061364]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:53.062811]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:53.064145]: Calling function.
#> ℹ [2024-08-04 14:44:53.065906]: Fitting sample: Sample_1
#> ℹ [2024-08-04 14:44:53.067444]: Fitting sample: Sample_2
#> ℹ [2024-08-04 14:44:53.068951]: Fitting sample: Sample_3
#> ℹ [2024-08-04 14:44:53.070498]: Fitting sample: Sample_4
#> ℹ [2024-08-04 14:44:53.071999]: Fitting sample: Sample_5
#> ℹ [2024-08-04 14:44:53.073534]: Fitting sample: Sample_6
#> ℹ [2024-08-04 14:44:53.075011]: Fitting sample: Sample_7
#> ℹ [2024-08-04 14:44:53.07654]: Fitting sample: Sample_8
#> ℹ [2024-08-04 14:44:53.078043]: Fitting sample: Sample_9
#> ℹ [2024-08-04 14:44:53.079506]: Fitting sample: Sample_10
#> ℹ [2024-08-04 14:44:53.080959]: Fitting sample: Sample_11
#> ℹ [2024-08-04 14:44:53.082431]: Fitting sample: Sample_12
#> ℹ [2024-08-04 14:44:53.083911]: Fitting sample: Sample_13
#> ℹ [2024-08-04 14:44:53.085437]: Fitting sample: Sample_14
#> ℹ [2024-08-04 14:44:53.086899]: Fitting sample: Sample_15
#> ℹ [2024-08-04 14:44:53.088344]: Fitting sample: Sample_16
#> ℹ [2024-08-04 14:44:53.089827]: Fitting sample: Sample_17
#> ℹ [2024-08-04 14:44:53.091295]: Fitting sample: Sample_18
#> ℹ [2024-08-04 14:44:53.092766]: Fitting sample: Sample_19
#> ℹ [2024-08-04 14:44:53.094285]: Fitting sample: Sample_20
#> ℹ [2024-08-04 14:44:53.095757]: Fitting sample: Sample_21
#> ℹ [2024-08-04 14:44:53.09727]: Fitting sample: Sample_22
#> ℹ [2024-08-04 14:44:53.098742]: Fitting sample: Sample_23
#> ℹ [2024-08-04 14:44:53.100275]: Fitting sample: Sample_24
#> ℹ [2024-08-04 14:44:53.101813]: Fitting sample: Sample_25
#> ℹ [2024-08-04 14:44:53.103574]: Fitting sample: Sample_26
#> ℹ [2024-08-04 14:44:53.105102]: Fitting sample: Sample_27
#> ℹ [2024-08-04 14:44:53.10664]: Fitting sample: Sample_28
#> ℹ [2024-08-04 14:44:53.108167]: Fitting sample: Sample_29
#> ℹ [2024-08-04 14:44:53.109751]: Fitting sample: Sample_30
#> ✔ [2024-08-04 14:44:53.111289]: Done.
#> ℹ [2024-08-04 14:44:53.112765]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:53.115199]: Done.
#> ℹ [2024-08-04 14:44:53.116843]: 0.07 secs elapsed.
v1
#> Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6
#> COSMIC_1 0.000 489.8588 209.7209 0.00000 0.0000 0.00000
#> COSMIC_2 0.000 4772.1359 790.7404 1141.34400 1260.9176 451.61921
#> COSMIC_3 9388.300 11304.1621 6409.2694 9437.97961 1368.1160 147.53218
#> COSMIC_4 0.000 0.0000 0.0000 0.00000 0.0000 240.12278
#> COSMIC_5 22269.534 0.0000 0.0000 0.00000 0.0000 0.00000
#> COSMIC_6 0.000 2257.8431 3298.0989 0.00000 0.0000 336.85671
#> COSMIC_7 0.000 0.0000 0.0000 0.00000 0.0000 0.00000
#> COSMIC_8 9477.314 0.0000 0.0000 0.00000 0.0000 379.85216
#> COSMIC_9 1624.851 0.0000 0.0000 0.00000 0.0000 10.06643
#> COSMIC_10 0.000 0.0000 62.1704 6.67638 65.9664 46.95054
#> Sample_7 Sample_8 Sample_9 Sample_10 Sample_11 Sample_12
#> COSMIC_1 28.74367 1215.66688 0.00000 0.00000 992.0793 0.0000
#> COSMIC_2 127.57118 248.22883 345.66245 1341.62106 866.9798 1382.2258
#> COSMIC_3 949.82786 59.47163 2109.15735 1104.17431 2267.4729 22983.0181
#> COSMIC_4 146.21151 450.56797 0.00000 868.66564 0.0000 7513.7174
#> COSMIC_5 0.00000 15.81582 0.00000 3114.99239 454.5275 15707.0752
#> COSMIC_6 205.95216 0.00000 0.00000 0.00000 674.9405 0.0000
#> COSMIC_7 0.00000 0.00000 65.11657 0.00000 0.0000 0.0000
#> COSMIC_8 0.00000 271.96232 0.00000 3037.45580 0.0000 0.0000
#> COSMIC_9 48.50970 40.22707 5604.06363 76.50516 0.0000 911.1828
#> COSMIC_10 90.18391 90.05947 0.00000 169.58564 0.0000 1470.7807
#> Sample_13 Sample_14 Sample_15 Sample_16 Sample_17 Sample_18
#> COSMIC_1 27.553530 0.0000 607.73052 0.0000 7142.931 450.8810
#> COSMIC_2 220.197356 1383.6365 1089.11552 249.5889 2234.646 428.5266
#> COSMIC_3 1803.765880 1913.0862 7718.95869 2417.0770 0.000 1803.5497
#> COSMIC_4 2.444918 0.0000 0.00000 2525.5503 0.000 0.0000
#> COSMIC_5 0.000000 793.4116 0.00000 1120.9350 11397.113 0.0000
#> COSMIC_6 0.000000 120.8657 0.00000 0.0000 4817.624 0.0000
#> COSMIC_7 0.000000 0.0000 0.00000 0.0000 0.000 0.0000
#> COSMIC_8 0.000000 0.0000 0.00000 593.4937 0.000 175.8705
#> COSMIC_9 0.000000 0.0000 1273.97434 321.6396 2080.685 2713.1722
#> COSMIC_10 63.038316 0.0000 98.22093 497.7156 0.000 0.0000
#> Sample_19 Sample_20 Sample_21 Sample_22 Sample_23 Sample_24
#> COSMIC_1 3442.8664 252.686817 521.6661 6532.753069 27.78616 585.9699
#> COSMIC_2 909.0835 6.731634 794.8881 0.000000 37.07453 3737.3080
#> COSMIC_3 3388.9789 0.000000 11487.9198 9577.877624 0.00000 40624.6240
#> COSMIC_4 5785.5234 643.570806 0.0000 0.000000 1646.68130 0.0000
#> COSMIC_5 17067.4485 1174.973238 0.0000 19202.665730 0.00000 0.0000
#> COSMIC_6 0.0000 0.000000 0.0000 2318.605839 532.00164 0.0000
#> COSMIC_7 0.0000 0.000000 0.0000 0.391064 0.00000 0.0000
#> COSMIC_8 647.0108 61.792741 426.2269 604.885135 733.46374 0.0000
#> COSMIC_9 391.0308 322.926794 0.0000 112.692931 1097.40415 0.0000
#> COSMIC_10 1260.0576 134.317970 101.2992 7.128609 337.58848 948.0980
#> Sample_25 Sample_26 Sample_27 Sample_28 Sample_29 Sample_30
#> COSMIC_1 1415.0938 1196.88834 127.7639 0.000000 522.352549 0.0000
#> COSMIC_2 1152.5880 199.49602 896.7186 9.999714 32.439082 0.0000
#> COSMIC_3 0.0000 1575.30113 8949.9313 0.000000 185.293182 0.0000
#> COSMIC_4 2893.4527 0.00000 0.0000 1009.607682 0.000000 0.0000
#> COSMIC_5 0.0000 0.00000 0.0000 1226.700289 1030.830037 1449.4794
#> COSMIC_6 827.5402 2436.90356 0.0000 0.000000 9.451177 559.2979
#> COSMIC_7 0.0000 0.00000 0.0000 0.000000 0.000000 0.0000
#> COSMIC_8 0.0000 0.00000 0.0000 433.980720 245.162304 369.9575
#> COSMIC_9 3201.4470 523.89832 0.0000 91.131812 1622.471669 540.2652
#> COSMIC_10 671.8784 12.51264 115.5862 201.579783 0.000000 0.0000
# If possible, auto-reduce the reference signatures
# for better fitting data from a sample
v2 = sig_fit(data, sig = ref, auto_reduce = TRUE)
#> ℹ [2024-08-04 14:44:53.120702]: Started.
#> ℹ [2024-08-04 14:44:53.122493]: Signature index not detected.
#> ✔ [2024-08-04 14:44:53.124123]: Signature matrix/data.frame detected.
#> ✔ [2024-08-04 14:44:53.125714]: Database and index checked.
#> ✔ [2024-08-04 14:44:53.127366]: Signature normalized.
#> ℹ [2024-08-04 14:44:53.128816]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:53.130289]: Checked.
#> ℹ [2024-08-04 14:44:53.131691]: Checking rownames for catalog matrix and signature matrix.
#> ℹ [2024-08-04 14:44:53.133116]: Matrix V and W don't have same orders. Try reordering...
#> ✔ [2024-08-04 14:44:53.13469]: Checked.
#> ✔ [2024-08-04 14:44:53.136127]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:53.137574]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:53.138984]: Calling function.
#> ℹ [2024-08-04 14:44:53.140747]: Fitting sample: Sample_1
#> ✔ [2024-08-04 14:44:53.142389]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.143843]: Fitting sample: Sample_2
#> ℹ [2024-08-04 14:44:53.145437]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.146953]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.148377]: Fitting sample: Sample_2
#> ✔ [2024-08-04 14:44:53.150042]: Stop optimizing at exposure level: 0.001, 6 signatures dropped.
#> ℹ [2024-08-04 14:44:53.151488]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.152912]: Fitting sample: Sample_3
#> ℹ [2024-08-04 14:44:53.154498]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.155961]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.157408]: Fitting sample: Sample_3
#> ✔ [2024-08-04 14:44:53.158954]: Stop optimizing at exposure level: 0.001, 5 signatures dropped.
#> ℹ [2024-08-04 14:44:53.160388]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.161865]: Fitting sample: Sample_4
#> ℹ [2024-08-04 14:44:53.163415]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.164878]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.166359]: Fitting sample: Sample_4
#> ✔ [2024-08-04 14:44:53.167873]: Stop optimizing at exposure level: 0.001, 8 signatures dropped.
#> ℹ [2024-08-04 14:44:53.169313]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.170739]: Fitting sample: Sample_5
#> ℹ [2024-08-04 14:44:53.172262]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.173745]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.175178]: Fitting sample: Sample_5
#> ✔ [2024-08-04 14:44:53.176693]: Stop optimizing at exposure level: 0.001, 7 signatures dropped.
#> ℹ [2024-08-04 14:44:53.178165]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.179597]: Fitting sample: Sample_6
#> ✔ [2024-08-04 14:44:53.18111]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.182583]: Fitting sample: Sample_7
#> ℹ [2024-08-04 14:44:53.184183]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.185669]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.187086]: Fitting sample: Sample_7
#> ✔ [2024-08-04 14:44:53.188588]: Stop optimizing at exposure level: 0.001, 3 signatures dropped.
#> ℹ [2024-08-04 14:44:53.190025]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.191432]: Fitting sample: Sample_8
#> ✔ [2024-08-04 14:44:53.192927]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.194384]: Fitting sample: Sample_9
#> ℹ [2024-08-04 14:44:53.195895]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.197356]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.198764]: Fitting sample: Sample_9
#> ✔ [2024-08-04 14:44:53.200272]: Stop optimizing at exposure level: 0.001, 6 signatures dropped.
#> ℹ [2024-08-04 14:44:53.201711]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.203138]: Fitting sample: Sample_10
#> ✔ [2024-08-04 14:44:53.204766]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.206229]: Fitting sample: Sample_11
#> ℹ [2024-08-04 14:44:53.207723]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.2092]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.210652]: Fitting sample: Sample_11
#> ✔ [2024-08-04 14:44:53.21227]: Stop optimizing at exposure level: 0.001, 5 signatures dropped.
#> ℹ [2024-08-04 14:44:53.21371]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.215138]: Fitting sample: Sample_12
#> ℹ [2024-08-04 14:44:53.216645]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.218119]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.219514]: Fitting sample: Sample_12
#> ✔ [2024-08-04 14:44:53.221049]: Stop optimizing at exposure level: 0.001, 4 signatures dropped.
#> ℹ [2024-08-04 14:44:53.222513]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.223946]: Fitting sample: Sample_13
#> ℹ [2024-08-04 14:44:53.225532]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.226982]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.2284]: Fitting sample: Sample_13
#> ✔ [2024-08-04 14:44:53.229973]: Stop optimizing at exposure level: 0.001, 5 signatures dropped.
#> ℹ [2024-08-04 14:44:53.231441]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.232901]: Fitting sample: Sample_14
#> ℹ [2024-08-04 14:44:53.234504]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.235968]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.237413]: Fitting sample: Sample_14
#> ✔ [2024-08-04 14:44:53.238938]: Stop optimizing at exposure level: 0.001, 6 signatures dropped.
#> ℹ [2024-08-04 14:44:53.240421]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.24226]: Fitting sample: Sample_15
#> ℹ [2024-08-04 14:44:53.244189]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.246016]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.247503]: Fitting sample: Sample_15
#> ✔ [2024-08-04 14:44:53.249068]: Stop optimizing at exposure level: 0.001, 5 signatures dropped.
#> ℹ [2024-08-04 14:44:53.250533]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.251994]: Fitting sample: Sample_16
#> ℹ [2024-08-04 14:44:53.253558]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.255]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.269706]: Fitting sample: Sample_16
#> ✔ [2024-08-04 14:44:53.271405]: Stop optimizing at exposure level: 0.001, 3 signatures dropped.
#> ℹ [2024-08-04 14:44:53.272815]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.274244]: Fitting sample: Sample_17
#> ✔ [2024-08-04 14:44:53.275723]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.277086]: Fitting sample: Sample_18
#> ℹ [2024-08-04 14:44:53.278585]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.27998]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.281373]: Fitting sample: Sample_18
#> ✔ [2024-08-04 14:44:53.282816]: Stop optimizing at exposure level: 0.001, 5 signatures dropped.
#> ℹ [2024-08-04 14:44:53.284176]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.285608]: Fitting sample: Sample_19
#> ℹ [2024-08-04 14:44:53.28707]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.288445]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.289822]: Fitting sample: Sample_19
#> ✔ [2024-08-04 14:44:53.291264]: Stop optimizing at exposure level: 0.001, 2 signatures dropped.
#> ℹ [2024-08-04 14:44:53.29262]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.294016]: Fitting sample: Sample_20
#> ℹ [2024-08-04 14:44:53.295506]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.296881]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.298263]: Fitting sample: Sample_20
#> ✔ [2024-08-04 14:44:53.299694]: Stop optimizing at exposure level: 0.001, 3 signatures dropped.
#> ℹ [2024-08-04 14:44:53.301047]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.302451]: Fitting sample: Sample_21
#> ℹ [2024-08-04 14:44:53.303922]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.305347]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.306699]: Fitting sample: Sample_21
#> ✔ [2024-08-04 14:44:53.308142]: Stop optimizing at exposure level: 0.001, 5 signatures dropped.
#> ℹ [2024-08-04 14:44:53.309547]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.310941]: Fitting sample: Sample_22
#> ✔ [2024-08-04 14:44:53.312412]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.313878]: Fitting sample: Sample_23
#> ℹ [2024-08-04 14:44:53.315367]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.316778]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.318177]: Fitting sample: Sample_23
#> ✔ [2024-08-04 14:44:53.319669]: Stop optimizing at exposure level: 0.001, 3 signatures dropped.
#> ℹ [2024-08-04 14:44:53.321039]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.322554]: Fitting sample: Sample_24
#> ℹ [2024-08-04 14:44:53.324054]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.325501]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.326874]: Fitting sample: Sample_24
#> ✔ [2024-08-04 14:44:53.328346]: Stop optimizing at exposure level: 0.001, 6 signatures dropped.
#> ℹ [2024-08-04 14:44:53.329754]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.331151]: Fitting sample: Sample_25
#> ℹ [2024-08-04 14:44:53.332627]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.334075]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.335469]: Fitting sample: Sample_25
#> ✔ [2024-08-04 14:44:53.336971]: Stop optimizing at exposure level: 0.001, 4 signatures dropped.
#> ℹ [2024-08-04 14:44:53.338402]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.339784]: Fitting sample: Sample_26
#> ✔ [2024-08-04 14:44:53.341301]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.342684]: Fitting sample: Sample_27
#> ℹ [2024-08-04 14:44:53.344161]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.345632]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.346998]: Fitting sample: Sample_27
#> ✔ [2024-08-04 14:44:53.348461]: Stop optimizing at exposure level: 0.001, 6 signatures dropped.
#> ℹ [2024-08-04 14:44:53.349887]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.351282]: Fitting sample: Sample_28
#> ℹ [2024-08-04 14:44:53.352774]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.35428]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.355667]: Fitting sample: Sample_28
#> ✔ [2024-08-04 14:44:53.357174]: Stop optimizing at exposure level: 0.001, 4 signatures dropped.
#> ℹ [2024-08-04 14:44:53.358587]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.359979]: Fitting sample: Sample_29
#> ℹ [2024-08-04 14:44:53.361498]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.362919]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.364282]: Fitting sample: Sample_29
#> ✔ [2024-08-04 14:44:53.365834]: Stop optimizing at exposure level: 0.001, 3 signatures dropped.
#> ℹ [2024-08-04 14:44:53.367232]: Cosine similarity with 0 improved.
#> ℹ [2024-08-04 14:44:53.36862]: Fitting sample: Sample_30
#> ℹ [2024-08-04 14:44:53.370151]: Start optimizing...
#> ℹ [2024-08-04 14:44:53.371586]: Dropping reference signatures with relative exposure <0.001
#> ℹ [2024-08-04 14:44:53.372959]: Fitting sample: Sample_30
#> ✔ [2024-08-04 14:44:53.374475]: Stop optimizing at exposure level: 0.001, 6 signatures dropped.
#> ℹ [2024-08-04 14:44:53.375848]: Cosine similarity with 0 improved.
#> ✔ [2024-08-04 14:44:53.377263]: Done.
#> ℹ [2024-08-04 14:44:53.378633]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:53.380875]: Done.
#> ℹ [2024-08-04 14:44:53.38249]: 0.262 secs elapsed.
v2
#> Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6 Sample_7
#> COSMIC_1 0.000 489.8588 209.7209 0.000 0.0000 0.00000 28.74367
#> COSMIC_2 0.000 4772.1359 790.7404 1141.894 1260.9176 451.61921 127.57118
#> COSMIC_3 9388.300 11304.1621 6409.2694 9444.106 1368.1160 147.53218 949.82786
#> COSMIC_4 0.000 0.0000 0.0000 0.000 0.0000 240.12278 146.21151
#> COSMIC_5 22269.534 0.0000 0.0000 0.000 0.0000 0.00000 0.00000
#> COSMIC_6 0.000 2257.8431 3298.0989 0.000 0.0000 336.85671 205.95216
#> COSMIC_7 0.000 0.0000 0.0000 0.000 0.0000 0.00000 0.00000
#> COSMIC_8 9477.314 0.0000 0.0000 0.000 0.0000 379.85216 0.00000
#> COSMIC_9 1624.851 0.0000 0.0000 0.000 0.0000 10.06643 48.50970
#> COSMIC_10 0.000 0.0000 62.1704 0.000 65.9664 46.95054 90.18391
#> Sample_8 Sample_9 Sample_10 Sample_11 Sample_12 Sample_13
#> COSMIC_1 1215.66688 0.00000 0.00000 992.0793 0.0000 27.553530
#> COSMIC_2 248.22883 345.66245 1341.62106 866.9798 1382.2258 220.197356
#> COSMIC_3 59.47163 2109.15735 1104.17431 2267.4729 22983.0181 1803.765880
#> COSMIC_4 450.56797 0.00000 868.66564 0.0000 7513.7174 2.444918
#> COSMIC_5 15.81582 0.00000 3114.99239 454.5275 15707.0752 0.000000
#> COSMIC_6 0.00000 0.00000 0.00000 674.9405 0.0000 0.000000
#> COSMIC_7 0.00000 65.11657 0.00000 0.0000 0.0000 0.000000
#> COSMIC_8 271.96232 0.00000 3037.45580 0.0000 0.0000 0.000000
#> COSMIC_9 40.22707 5604.06363 76.50516 0.0000 911.1828 0.000000
#> COSMIC_10 90.05947 0.00000 169.58564 0.0000 1470.7807 63.038316
#> Sample_14 Sample_15 Sample_16 Sample_17 Sample_18 Sample_19
#> COSMIC_1 0.0000 607.73052 0.0000 7142.931 450.8810 3442.8664
#> COSMIC_2 1383.6365 1089.11552 249.5889 2234.646 428.5266 909.0835
#> COSMIC_3 1913.0862 7718.95869 2417.0770 0.000 1803.5497 3388.9789
#> COSMIC_4 0.0000 0.00000 2525.5503 0.000 0.0000 5785.5234
#> COSMIC_5 793.4116 0.00000 1120.9350 11397.113 0.0000 17067.4485
#> COSMIC_6 120.8657 0.00000 0.0000 4817.624 0.0000 0.0000
#> COSMIC_7 0.0000 0.00000 0.0000 0.000 0.0000 0.0000
#> COSMIC_8 0.0000 0.00000 593.4937 0.000 175.8705 647.0108
#> COSMIC_9 0.0000 1273.97434 321.6396 2080.685 2713.1722 391.0308
#> COSMIC_10 0.0000 98.22093 497.7156 0.000 0.0000 1260.0576
#> Sample_20 Sample_21 Sample_22 Sample_23 Sample_24 Sample_25
#> COSMIC_1 252.686817 521.6661 6532.753069 27.78616 585.9699 1415.0938
#> COSMIC_2 6.731634 794.8881 0.000000 37.07453 3737.3080 1152.5880
#> COSMIC_3 0.000000 11487.9198 9577.877624 0.00000 40624.6240 0.0000
#> COSMIC_4 643.570806 0.0000 0.000000 1646.68130 0.0000 2893.4527
#> COSMIC_5 1174.973238 0.0000 19202.665730 0.00000 0.0000 0.0000
#> COSMIC_6 0.000000 0.0000 2318.605839 532.00164 0.0000 827.5402
#> COSMIC_7 0.000000 0.0000 0.391064 0.00000 0.0000 0.0000
#> COSMIC_8 61.792741 426.2269 604.885135 733.46374 0.0000 0.0000
#> COSMIC_9 322.926794 0.0000 112.692931 1097.40415 0.0000 3201.4470
#> COSMIC_10 134.317970 101.2992 7.128609 337.58848 948.0980 671.8784
#> Sample_26 Sample_27 Sample_28 Sample_29 Sample_30
#> COSMIC_1 1196.88834 127.7639 0.000000 522.352549 0.0000
#> COSMIC_2 199.49602 896.7186 9.999714 32.439082 0.0000
#> COSMIC_3 1575.30113 8949.9313 0.000000 185.293182 0.0000
#> COSMIC_4 0.00000 0.0000 1009.607682 0.000000 0.0000
#> COSMIC_5 0.00000 0.0000 1226.700289 1030.830037 1449.4794
#> COSMIC_6 2436.90356 0.0000 0.000000 9.451177 559.2979
#> COSMIC_7 0.00000 0.0000 0.000000 0.000000 0.0000
#> COSMIC_8 0.00000 0.0000 433.980720 245.162304 369.9575
#> COSMIC_9 523.89832 0.0000 91.131812 1622.471669 540.2652
#> COSMIC_10 12.51264 115.5862 201.579783 0.000000 0.0000
all.equal(v1, v2)
#> [1] "Mean relative difference: 0.001157504"
# Some samples reported signatures dropped
# but its original activity values are 0s,
# so the data remain same (0 -> 0)
all.equal(v1[, 2], v2[, 2])
#> [1] TRUE
# For COSMIC_10, 6.67638 -> 0
v1[, 4]; v2[, 4]
#> COSMIC_1 COSMIC_2 COSMIC_3 COSMIC_4 COSMIC_5 COSMIC_6 COSMIC_7
#> 0.00000 1141.34400 9437.97961 0.00000 0.00000 0.00000 0.00000
#> COSMIC_8 COSMIC_9 COSMIC_10
#> 0.00000 0.00000 6.67638
#> COSMIC_1 COSMIC_2 COSMIC_3 COSMIC_4 COSMIC_5 COSMIC_6 COSMIC_7 COSMIC_8
#> 0.000 1141.894 9444.106 0.000 0.000 0.000 0.000 0.000
#> COSMIC_9 COSMIC_10
#> 0.000 0.000
all.equal(v1[, 4], v2[, 4])
#> [1] "Mean relative difference: 0.00126136"
# For general purpose -----------------------
W <- matrix(c(1, 2, 3, 4, 5, 6), ncol = 2)
colnames(W) <- c("sig1", "sig2")
W <- apply(W, 2, function(x) x / sum(x))
H <- matrix(c(2, 5, 3, 6, 1, 9, 1, 2), ncol = 4)
colnames(H) <- paste0("samp", 1:4)
V <- W %*% H
V
#> samp1 samp2 samp3 samp4
#> [1,] 1.666667 2.1 2.566667 0.7
#> [2,] 2.333333 3.0 3.333333 1.0
#> [3,] 3.000000 3.9 4.100000 1.3
if (requireNamespace("quadprog", quietly = TRUE)) {
H_infer <- sig_fit(V, W, method = "QP")
H_infer
H
H_dt <- sig_fit(V, W, method = "QP", auto_reduce = TRUE, return_class = "data.table")
H_dt
## Show results
show_sig_fit(H_infer)
show_sig_fit(H_dt)
## Get clusters/groups
H_dt_rel <- sig_fit(V, W, return_class = "data.table", type = "relative")
z <- get_groups(H_dt_rel, method = "k-means")
show_groups(z)
}
#> ℹ [2024-08-04 14:44:53.394578]: Started.
#> ℹ [2024-08-04 14:44:53.396351]: Signature index not detected.
#> ✔ [2024-08-04 14:44:53.397891]: Signature matrix/data.frame detected.
#> ✔ [2024-08-04 14:44:53.399314]: Database and index checked.
#> ✔ [2024-08-04 14:44:53.400762]: Signature normalized.
#> ℹ [2024-08-04 14:44:53.40214]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:53.403488]: Checked.
#> ✔ [2024-08-04 14:44:53.4051]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:53.406483]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:53.407822]: Calling function.
#> ℹ [2024-08-04 14:44:53.40954]: Fitting sample: samp1
#> ℹ [2024-08-04 14:44:53.411074]: Fitting sample: samp2
#> ℹ [2024-08-04 14:44:53.412497]: Fitting sample: samp3
#> ℹ [2024-08-04 14:44:53.413974]: Fitting sample: samp4
#> ✔ [2024-08-04 14:44:53.415424]: Done.
#> ℹ [2024-08-04 14:44:53.416785]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:53.418723]: Done.
#> ℹ [2024-08-04 14:44:53.420151]: 0.026 secs elapsed.
#> ℹ [2024-08-04 14:44:53.421618]: Started.
#> ℹ [2024-08-04 14:44:53.42296]: Signature index not detected.
#> ✔ [2024-08-04 14:44:53.424321]: Signature matrix/data.frame detected.
#> ✔ [2024-08-04 14:44:53.425695]: Database and index checked.
#> ✔ [2024-08-04 14:44:53.427125]: Signature normalized.
#> ℹ [2024-08-04 14:44:53.428476]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:53.42989]: Checked.
#> ✔ [2024-08-04 14:44:53.431218]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:53.432547]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:53.433916]: Calling function.
#> ℹ [2024-08-04 14:44:53.435509]: Fitting sample: samp1
#> ✔ [2024-08-04 14:44:53.437042]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.438488]: Fitting sample: samp2
#> ✔ [2024-08-04 14:44:53.439959]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.441366]: Fitting sample: samp3
#> ✔ [2024-08-04 14:44:53.442826]: The cosine similarity is very high, just return result.
#> ℹ [2024-08-04 14:44:53.444197]: Fitting sample: samp4
#> ✔ [2024-08-04 14:44:53.445733]: The cosine similarity is very high, just return result.
#> ✔ [2024-08-04 14:44:53.447104]: Done.
#> ℹ [2024-08-04 14:44:53.448448]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:53.458266]: Done.
#> ℹ [2024-08-04 14:44:53.460099]: 0.038 secs elapsed.
#> ℹ [2024-08-04 14:44:53.461886]: Started.
#> ℹ [2024-08-04 14:44:53.463283]: Checking input format.
#> ✔ [2024-08-04 14:44:53.472363]: Checked.
#> ℹ [2024-08-04 14:44:53.474108]: Checking filters.
#> ℹ [2024-08-04 14:44:53.475566]: Checked.
#> ℹ [2024-08-04 14:44:53.480137]: Plotting.
#> ℹ [2024-08-04 14:44:53.514821]: 0.053 secs elapsed.
#> ℹ [2024-08-04 14:44:53.516798]: Started.
#> ℹ [2024-08-04 14:44:53.518325]: Checking input format.
#> ✔ [2024-08-04 14:44:53.519788]: Checked.
#> ℹ [2024-08-04 14:44:53.521174]: Checking filters.
#> ℹ [2024-08-04 14:44:53.522582]: Checked.
#> ℹ [2024-08-04 14:44:53.527352]: Plotting.
#> ℹ [2024-08-04 14:44:53.560861]: 0.044 secs elapsed.
#> ℹ [2024-08-04 14:44:53.562776]: Started.
#> ℹ [2024-08-04 14:44:53.564254]: Signature index not detected.
#> ✔ [2024-08-04 14:44:53.565683]: Signature matrix/data.frame detected.
#> ✔ [2024-08-04 14:44:53.567054]: Database and index checked.
#> ✔ [2024-08-04 14:44:53.568487]: Signature normalized.
#> ℹ [2024-08-04 14:44:53.569924]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:44:53.571286]: Checked.
#> ✔ [2024-08-04 14:44:53.572623]: Method 'QP' detected.
#> ✔ [2024-08-04 14:44:53.574]: Corresponding function generated.
#> ℹ [2024-08-04 14:44:53.575338]: Calling function.
#> ℹ [2024-08-04 14:44:53.576908]: Fitting sample: samp1
#> ℹ [2024-08-04 14:44:53.578411]: Fitting sample: samp2
#> ℹ [2024-08-04 14:44:53.57983]: Fitting sample: samp3
#> ℹ [2024-08-04 14:44:53.581251]: Fitting sample: samp4
#> ✔ [2024-08-04 14:44:53.582856]: Done.
#> ℹ [2024-08-04 14:44:53.584222]: Generating output signature exposures.
#> ✔ [2024-08-04 14:44:53.59396]: Done.
#> ℹ [2024-08-04 14:44:53.595741]: 0.033 secs elapsed.
#> ℹ [2024-08-04 14:44:53.597293]: Started.
#> ✔ [2024-08-04 14:44:53.598678]: A 'data.table' detected.
#> ✔ [2024-08-04 14:44:53.600028]: Method checked.
#> ✔ [2024-08-04 14:44:53.601605]: Exposure should be relative checked.
#> ℹ [2024-08-04 14:44:53.603197]: Running k-means with 2 clusters...
#> ℹ [2024-08-04 14:44:53.605265]: Generating a table of group and signature contribution (stored in 'map_table' attr):
#> sig1 sig2
#> 1 0.31746 0.68254
#> 2 0.10000 0.90000
#> ℹ [2024-08-04 14:44:53.606779]: Assigning a group to a signature with the maximum fraction...
#> ℹ [2024-08-04 14:44:53.610518]: Summarizing...
#> group #1: 3 samples with sig2 enriched.
#> group #2: 1 samples with sig2 enriched.
#> ! [2024-08-04 14:44:53.612502]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
#> ℹ [2024-08-04 14:44:53.613947]: 0.017 secs elapsed.
# if (requireNamespace("GenSA", quietly = TRUE)) {
# H_infer <- sig_fit(V, W, method = "SA")
# H_infer
# H
#
# H_dt <- sig_fit(V, W, method = "SA", return_class = "data.table")
# H_dt
#
# ## Modify arguments to method
# sig_fit(V, W, method = "SA", maxit = 10, temperature = 100)
#
# ## Show results
# show_sig_fit(H_infer)
# show_sig_fit(H_dt)
# }
# }