fitSignatures {MesKit} | R Documentation |
Find nonnegative linear combination of mutation signatures to reconstruct matrix and calculate cosine similarity based on somatic SNVs.
fitSignatures( tri_matrix = NULL, patient.id = NULL, signaturesRef = "cosmic_v2", associated = NULL, min.mut.count = 15, signature.cutoff = 0.1 )
tri_matrix |
A matrix or a list of matrix generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included |
signaturesRef |
Signature reference,Users can upload their own reference. Default "cosmic_v2". Option: "exome_cosmic_v3","nature2013". |
associated |
Associated Vector of associated signatures. If given, will narrow the signatures reference to only the ones listed. Default NULL. |
min.mut.count |
The threshold for the variants in a branch. Default 15. |
signature.cutoff |
Discard any signature relative contributions with a weight less than this amount. Default 0.1. |
A list of data frames, each one contains treeMSOutput, containing information about each set/branch's mutational signature.
maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit") clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit") ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit") maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19") ## Load a reference genome. library(BSgenome.Hsapiens.UCSC.hg19) phyloTree <- getPhyloTree(maf, patient.id = 'V402') tri_matrix <- triMatrix(phyloTree) fitSignatures(tri_matrix)