extractSignatures: Extract mutational signatures from trinucletide context.

Description

Decompose a matrix of 96 substitution classes into n signatures.

Usage

extractSignatures(mat, n = NULL, nTry = 6, plotBestFitRes = FALSE,
  parallel = NULL)

Arguments

mat

Input matrix of diemnsion nx96 generated by trinucleotideMatrix

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.

nTry

tries upto this number of signatures before choosing best n. Default 6.

plotBestFitRes

plots consensus heatmap for range of values tried. Default FALSE

parallel

calls to .opt argument of nmf. e.g, 'P4' for using 4 cores. See note on nmf for MAC users.

Value

a list with decomposed scaled signatures, signature contributions in each sample and a correlatoon table against validated signatures.

Details

This function decomposes a non-negative matrix into n signatures. Extracted signatures are compared against 21 experimentally validated signatures by calculating correlation coefficient. See http://www.nature.com/nature/journal/v500/n7463/fig_tab/nature12477_F2.html for details.

Examples

Run this code

# 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)
# }