Extract mutational signatures from 96 mutation matrix using NMF

Description

Decomposes trinucleotide count matrix into signatures and contribution of those signatures to the spectra of the samples/vcf files.

Usage

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Arguments

mut_matrix

96 mutation count matrix

rank

Number of signatures to extract

nrun

Number of iterations, default = 200

Value

Named list of mutation matrix, signatures and signature contribution

See Also

mut_matrix

Examples

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## See the 'mut_matrix()' example for how we obtained the mutation matrix:
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
                    package="MutationalPatterns"))

## This function is computational intensive.
# nmf_res <- extract_signatures(mut_mat, rank = 2)

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