maf2cat: Generate Mutation Catalog from MAF file

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

Generate Mutation Catalog from MAF file

Description

Input is MAF file and the corresponding trinucleotide catalog matrix is generated

Usage

maf2cat(maf, progress.bar = TRUE)

Arguments

maf	MAF file name or data frame. It must contain a column named Ref_Tri containing the trinucleotide sequences surrounding the mutation site. If the mutation site reference allele is A, G, the Ref_Tri is the complement sequence of the trinucleotides, such that its central allele is always C, T.
progress.bar	Display progress bar

Value

Count matrix with mutation contexts in rows and Tumor_Sample_Barcode in columns.

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