RunMutPat: RunMutPat

In cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts

RunMutPat

Description

Identifies mutational signatures using Mutational Patterns

Usage

RunMutPat(mut.pat.input, df.mut.pat.ref.sigs, target.mut.sigs, verbose = TRUE)

Arguments

mut.pat.input	A list from MutPatParseVCFObj
df.mut.pat.ref.sigs	A data.frame returned by MutPatParseRefMutSigs
target.mut.sigs	A character vector of target mutational signatures names
verbose	If true, provides process details

Value

A list with the following elements

• tumor.mutation.types.spectrumA numeric vector of length 96 - 'observed' spectrum

• identified.mutation.types.spectrumA numeric vector of length 96 - 'identified' spectrum

• residualsA numeric vector of length 96 - residuals

• mutation.typesA character vector of length 96

• identified.mut.sigsA character vector where each element is a mutational signature identified

• identified.mut.sigs.contribution.weightsA numeric vector where each element is the weight of mutational signature identified. The ordering follows identified.mut.sigs

• cosine.similarity.scoreA numeric value

Examples

## Not run: 
vcf.obj <- ReadVCF(vcf.file = "../data/sample/HNT-082-BT.final.call.vcf", genome = "hg19")
df.ref.mut.sigs <- GetPCAWGMutSigs()
target.mut.sigs <- GetPCAWGMutSigsNames()
RunMutPat(vcf.obj = vcf.obj,
df.ref.mut.sigs = df.ref.mut.sigs,
target.mut.sigs = target.mut.sigs)

## End(Not run)

cgab-ncc/FIREVAT documentation built on Nov. 19, 2022, 5:55 p.m.