setMaf: Set Operations for MAF objects

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Set Operations for MAF objects

Usage

setdiffMAF(x, y, mafObj = TRUE, refAltMatch = TRUE, ...)

intersectMAF(x, y, refAltMatch = TRUE, mafObj = TRUE, ...)

Arguments

x	the first 'MAF' object.
y	the second 'MAF' object.
mafObj	Return output as an 'MAF' object. Default 'TRUE'
refAltMatch	Set operations are done by matching ref and alt alleles in addition to loci (Default). Id FALSE only loci (chr, start, end positions) are matched.
...	other parameters passing to 'subsetMaf' for subsetting operations.

Value

subset table or an object of class MAF-class. If no overlaps found returns 'NULL'

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
x <- subsetMaf(maf = laml, tsb = c('TCGA-AB-3009'))
y <- subsetMaf(maf = laml, tsb = c('TCGA-AB-2933'))
setdiffMAF(x, y)
intersectMAF(x, y) #Should return NULL due to no common variants

maftools documentation built on Feb. 6, 2021, 2 a.m.