mutFilterNormalDP: mutFilterNormalDP

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

mutFilterNormalDP

Description

Filter dbsnp/non-dbsnp variants based on their normal depth. Variants in dbSNP database should have normal depth >= 19, while non-dbSNP variants should have normal depth >= 8 to avoid being filtered.

Usage

mutFilterNormalDP(maf, dbsnpCutoff = 19, nonCutoff = 8, verbose = TRUE)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
dbsnpCutoff	Cutoff of normal depth for dnSNP variants. Default: 19.
nonCutoff	Cutoff of normal depth for non-dnSNP variants. Default: 8.
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame where some variants has N tag in CaTag column for Normal depth filtration.

Examples

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

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