processMut: processMut

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

processMut

Description

Takes union or intersection on multiple MAF data frame, and return 7 important columns.

Usage

processMut(mafList, processMethod = "union")

Arguments

mafList	A list of MAF data frames after going through at least one CaMutQC filtration function, and the length of the list <= 3.
processMethod	Methods for processing mutations, including "union" and "intersection". Default: "union".

Value

A data frame includes mutations after taking union or intersection.

Examples

maf_MuSE <- vcfToMAF(system.file("extdata/Multi-caller",
"WES_EA_T_1.MuSE.vep.vcf", package="CaMutQC"))
maf_MuSE_f <- mutFilterCom(maf_MuSE, report=FALSE, TMB=FALSE,
PONfile=system.file("extdata", "PON_test.txt", package="CaMutQC"), 
PONformat="txt")
maf_VarScan2 <- vcfToMAF(system.file("extdata/Multi-caller",
"WES_EA_T_1_varscan_filter_snp.vep.vcf", package="CaMutQC"))
maf_VarScan2_f <- mutFilterCom(maf_VarScan2, report=FALSE, TMB=FALSE,
PONfile=system.file("extdata", "PON_test.txt", package="CaMutQC"), 
PONformat="txt")
mafs <- list(maf_MuSE_f, maf_VarScan2_f)
maf_union <- processMut(mafs, processMethod="union")

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