mutFilterReg: mutFilterReg

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

mutFilterReg

Description

Filter variants not in specific regions.

Usage

mutFilterReg(
  maf,
  bedFile = NULL,
  bedHeader = FALSE,
  bedFilter = TRUE,
  verbose = TRUE
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
bedFile	A bed file that contains region information. Default: NULL
bedHeader	Whether the input bed file has a header or not. Default: FALSE.
bedFilter	Whether to filter the information in bed file or not, which only leaves segments in Chr1-Ch22, ChrX and ChrY. Default: TRUE
verbose	Whether to generate message/notification during the filtration process. Default: TRUE.

Value

An MAF data frame where some variants have R tag in CaTag column for region filtration.

Examples

maf <- vcfToMAF(system.file("extdata", "WES_EA_T_1_mutect2.vep.vcf",
package="CaMutQC"))
mafF <- mutFilterReg(maf, bedFile=system.file("extdata/bed/panel_hg38",
"Pan-cancer-hg38.rds", package="CaMutQC"))

likelet/CaMutQC documentation built on April 3, 2024, 9:06 a.m.