RunMutalisk: RunMutalisk

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

RunMutalisk

Description

Identifies mutational signatures using Mutalisk

Usage

RunMutalisk(
  vcf.obj,
  df.ref.mut.sigs,
  target.mut.sigs,
  random.sampling.candidate.mut.sigs = c(),
  method = "random.sampling",
  n.sample = 20,
  n.iter = 10,
  verbose = TRUE
)

Arguments

vcf.obj	A list (from firevat_vcf::ReadVCF)
df.ref.mut.sigs	A data.frame of reference mutational signatures
target.mut.sigs	A character vector of target mutational signatures names to identify from
random.sampling.candidate.mut.sigs	A character vector of mutational signatures names that gets appended to the list of candidate mutational signatures so that these are always considered.
method	A string value (must be either 'random.sampling' or 'all'). The method 'random.sampling' samples (without replacement) 'n.sample' number of signatures 'n.iter' number of times and runs the candidate signatures one last time. The method 'all' uses all target.mut.sigs
n.sample	An integer value ('random.sampling' method parameter) Number of signatures to choose for each iteration of random sampling).
n.iter	An integer value ('random.sampling' method parameter). Number of iterations to perform random sampling.
verbose	If true, provides process details

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.