Extract mutational signatures from trinucleotide context.
Decompose a matrix of 96 substitution classes into n signatures.
extractSignatures( mat, n = NULL, plotBestFitRes = FALSE, parallel = 4, pConstant = NULL )
mat |
Input matrix of diemnsion nx96 generated by |
n |
decompose matrix into n signatures. Default NULL. Tries to predict best value for |
plotBestFitRes |
plots consensus heatmap for range of values tried. Default FALSE |
parallel |
Default 4. Number of cores to use. |
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.
a list with decomposed scaled signatures, signature contributions in each sample and NMF object.
## Not run:
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', prefix = 'chr',
add = TRUE, useSyn = TRUE)
library("NMF")
laml.sign <- extractSignatures(mat = laml.tnm, plotBestFitRes = FALSE, n = 2, pConstant = 0.01)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.