fitSignatures: fitSignatures

In Niinleslie/MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

Find nonnegative linear combination of mutation signatures to reconstruct matrix and calculate cosine similarity based on somatic SNVs.

Usage

fitSignatures(
  tri_matrix = NULL,
  patient.id = NULL,
  signaturesRef = "cosmic_v2",
  associated = NULL,
  min.mut.count = 15,
  signature.cutoff = 0.1
)

Arguments

tri_matrix	A matrix or a list of matrix generated by triMatrix function.
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.

Value

A list of data frames, each one contains treeMSOutput, containing information about each set/branch's mutational signature.

Examples

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)

Niinleslie/MesKit documentation built on Jan. 29, 2022, 10:24 a.m.