R: Extract mutational signatures from trinucleotide context.

extractSignatures {maftools}

R Documentation

Extract mutational signatures from trinucleotide context.

Description

Decompose a matrix of 96 substitution classes into n signatures.

Usage

extractSignatures(
  mat,
  n = NULL,
  plotBestFitRes = FALSE,
  parallel = 4,
  pConstant = NULL
)

Arguments

`mat`	Input matrix of diemnsion nx96 generated by `trinucleotideMatrix`
`n`	decompose matrix into n signatures. Default NULL. Tries to predict best value for `n` by running NMF on a range of values and chooses based on cophenetic correlation coefficient.
`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 `non-conformable arrays` error

Details

This function decomposes a non-negative matrix into n signatures.

Value

a list with decomposed scaled signatures, signature contributions in each sample and NMF object.

Examples

## 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)

[Package maftools version 2.3.30 Index]