mutFilterSB: mutFilterSB

In likelet/CaMutQC: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

mutFilterSB

Description

Filter variants based on strand bias.

Usage

mutFilterSB(maf, method = "SOR", SBscore = 3)

Arguments

maf	An MAF object, generated by vcfToMAF function.
method	Method will be used to detect strand bias, including 'SOR' and 'Fisher'. Default: 'SOR'. SOR: StrandOddsRatio (https://gatk.broadinstitute.org/hc/en-us/articles/360041849111- StrandOddsRatio) Fisher's Exat Test: Switch to Phred socre (https://gatk.broadinstitute.org/hc/en-us/articles/360035532152-Fisher- s-Exact-Test)
SBscore	Cutoff strand bias score used to filter variants. Default: 3

Value

An MAF data frame where some variants have S tag in CaTag column for strand bias filtration

Examples

maf <- vcfToMAF(system.file("extdata",
"WES_EA_T_1_mutect2.vep.vcf", package="CaMutQC"))
mafF <- mutFilterSB(maf)

likelet/CaMutQC documentation built on Aug. 17, 2024, 4 a.m.