RunMutaliskHelper: RunMutaliskHelper

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

RunMutaliskHelper

Description

Helper function for RunMutalisk

Usage

RunMutaliskHelper(vcf.trinucleotide.data, df.ref.mut.sigs, target.mut.sigs)

Arguments

vcf.trinucleotide.data	A data.frame (from firevat_mutalisk::MutaliskParseVCFObj)
df.ref.mut.sigs	A data.frame of reference mutational signatures
target.mut.sigs	A character vector of target mutational signatures names

Value

A list with the following elements

• num.point.mutationsAn integer value - count of total point mutations

• sub.typesA character vector of length 96

• sub.types.spectrumA numeric vector of length 96

• num.mut.sigsAn integer value (count of unique mutational signatures identified)

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

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

• identified.mut.sigs.spectrumA numeric vector of length 96

• residualsA numeric vector of length 96

• rssA numeric value (residual sum of squares)

• cos.sim.scoreA numeric value (cosine similarity score between observed mutational spectrum and reconstructed mutational signatures)

• all.models.sigsA list where each element is a model; a model is a list of signatures identified)

• all.models.sigs.probsA list where each element is a model; a model is a list of contribution probabilities

• all.models.cos.sim.scoresA list where each element is a model; a model is a list of cosine similarity socres

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