maf2cat3: Construct catalog matix from MAF file (without of Ref_Tri...

In mskcc/tempoSig: Maximum Likelihood Fitting of Mutational Catalogs and De Novo Inference of Signatures

Construct catalog matix from MAF file (without of Ref_Tri column)

Description

Construct catalog matix from MAF file (without of Ref_Tri column)

Usage

maf2cat3(maf, ref.genome, fix.chr = TRUE, progress.bar = TRUE)

Arguments

maf	MAF file or data frame of chromosome, position, ref, and alt alleles
ref.genome	Reference genome of class BSgenome
fix.chr	Modify chromosome names into chr1, chr2, ... for ref.genome
progress.bar	Display progress bar

Value

Catalog matrix

Examples

library(BSgenome.Hsapiens.UCSC.hg19)
maf <- system.file('extdata', 'brca.maf', package = 'tempoSig')
x <- maf2cat3(maf, BSgenome.Hsapiens.UCSC.hg19)
head(x)

mskcc/tempoSig documentation built on Feb. 3, 2023, 8:35 a.m.