CheckIfVariantRefinementIsNecessary: CheckIfVariantRefinementIsNecessary

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

CheckIfVariantRefinementIsNecessary

Description

Checks if variant refinement is necessary by identifying mutational signatures related to sequencing artifact in the vcf.obj (set of original unrefined point mutations).

Usage

CheckIfVariantRefinementIsNecessary(
  vcf.obj,
  bsg,
  df.mut.pat.ref.sigs,
  target.mut.sigs,
  sequencing.artifact.mut.sigs,
  init.artifact.stop = 0.05,
  verbose = TRUE
)

Arguments

vcf.obj	A list from ReadVCF
bsg	BSgenome.Hsapiens.UCSC object
df.mut.pat.ref.sigs	A data.frame from MutPatParseRefMutSigs
target.mut.sigs	A character vector of target mutational signatures from reference mutational signatures.
sequencing.artifact.mut.sigs	A character vector of sequencing artifact mutational signatures from reference mutational signatures.
init.artifact.stop	Numeric value less than 1. If the sum of sequencing artifact weights in vcf.obj is less than or equal to this value then this function returns judgment = FALSE, otherwise returns judgment = TRUE.
verbose	If TRUE, provides process detail. Default value is TRUE.

Value

A list with the following elements

• judgmentA boolean value

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

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