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,
      nmf_type = c("regular", "variational_bayes"),
      single_core = FALSE
    )

### Arguments

`mut_matrix` | 96 mutation count matrix
`rank` | Number of signatures to extract
`nrun` | Number of iterations, default = 200. A lower number will be faster, but result in less accurate results.
`nmf_type` | Type of NMF to be used. Possible values: * 'regular' * 'variational_bayes' The 'regular' method comes from the NMF package. The 'variational_bayes' method comes from the ccfindR package. This method uses bayesian inference, which makes it easier to determine the mathmatically optimal number of signatures.
`single_core` | Boolean. If TRUE, it forces the NMF algorithm to use only a single core. This can sometimes prevent issues. Doesn't apply to variational-bayes NMF

### 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 computationally intensive.
    # nmf_res <- extract_signatures(mut_mat, rank = 2)

    ## It's also possible to use a variational Bayes method.
    ## It requires the ccfindR package to work.
    # nmf_res <- extract_signatures(mut_mat, rank = 2, nmf_type = "variational_bayes")

[Package MutationalPatterns version 3.0.1 Index]