extract_signatures: Extract mutational signatures from 96 mutation matrix using...
In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description Usage Arguments Value See Also Examples

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

extract_signatures(
  mut_matrix,
  rank,
  nrun = 200,
  nmf_type = c("regular", "variational_bayes"),
  single_core = FALSE
)

`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

Named list of mutation matrix, signatures and signature contribution

mut_matrix

## 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")