extractSignatures {maftools} | R Documentation |
Decompose a matrix of 96 substitution classes into n
signatures.
extractSignatures(mat, n = NULL, nTry = 6, plotBestFitRes = FALSE, parallel = NULL, pConstant = NULL)
mat |
Input matrix of diemnsion nx96 generated by |
n |
decompose matrix into n signatures. Default NULL. Tries to predict best value for |
nTry |
tries upto this number of signatures before choosing best |
plotBestFitRes |
plots consensus heatmap for range of values tried. Default FALSE |
parallel |
calls to .opt argument of |
pConstant |
A small positive value to add to the matrix. Use it ONLY if the functions throws an |
This function decomposes a non-negative matrix into n signatures. Extracted signatures are compared against 30 experimentally validated signatures by calculating cosine similarity. See http://cancer.sanger.ac.uk/cosmic/signatures for details.
a list with decomposed scaled signatures, signature contributions in each sample and a cosine similarity table against validated signatures.
trinucleotideMatrix
plotSignatures
## Not run: laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'hg19.fa', prefix = 'chr', add = TRUE, useSyn = TRUE) laml.sign <- extractSignatures(mat = laml.tnm, plotBestFitRes = FALSE) ## End(Not run)