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.

See Also

trinucleotideMatrix plotSignatures compareSignatures

Examples

## 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)

[Package maftools version 2.2.10 Index]