extract_signatures {MutationalPatterns} | R Documentation |
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
## 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")