GetGASuggestedSolutions: GetGASuggestedSolutions

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

GetGASuggestedSolutions

Description

Computes suggested solutions

Usage

GetGASuggestedSolutions(
  vcf.obj,
  bsg,
  config.obj,
  lower.upper.list,
  df.mut.pat.ref.sigs,
  target.mut.sigs,
  sequencing.artifact.mut.sigs,
  objective.fn,
  original.muts.seq.art.weights.sum,
  ga.preemptive.killing,
  verbose = TRUE
)

Arguments

vcf.obj	A list from ReadVCF
bsg	BSgenome.Hsapiens.UCSC object
config.obj	A list from ParseConfigFile
lower.upper.list	A list from GetParameterLowerUpperVector
df.mut.pat.ref.sigs	A data.frame from MutPatParseRefMutSigs
target.mut.sigs	A character vector of the target mutational signatures from reference mutational signatures.
sequencing.artifact.mut.sigs	A character vector of the sequencing artifact mutational signatures from reference mutational signatures.
objective.fn	Objective value derivation function.
original.muts.seq.art.weights.sum	A numeric value. 'seq.art.sigs.weights.sum' from CheckIfVariantRefinementIsNecessary
ga.preemptive.killing	If TRUE, then preemptively kills populations that yield greater sequencing artifact weights sum compared to the original mutatational signatures analysis
verbose	If TRUE, provides process detail. Default value is TRUE.

Value

A list with the following elements

• judgmentA boolean value

• seq.art.sigs.weightsA numeric value. Sum of sequencing artifact weights.

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