extract_signatures {MutationalPatterns} | R Documentation

## 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

    extract_signatures(mut_matrix, rank, nrun = 200)

### 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

    ## 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)

[Package MutationalPatterns version 1.12.0 Index]