extract_signatures: Extract mutational signatures from 96 mutation matrix using...

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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,
  fudge = NULL,
  seed = 123456
)

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 mathematically 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
fudge	Small positive number that is used for the variational_bayes NMF. Setting this to a small value like 0.0001 can prevent errors from occurring, when extracting many signatures at once. In general, we recommend extracting less signatures when errors occur, but this parameter can be used when that is not an option. Default = NULL.
seed	Random seed used for the regular NMF, default = 123456

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")

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.