setdiffMAF {maftools} | R Documentation

## Set Operations for MAF objects

### 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). If 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

[Package maftools version 2.10.05 Index]