Set Operations for MAF objects
Set Operations for MAF objects
setdiffMAF(x, y, mafObj = TRUE, refAltMatch = TRUE, ...) intersectMAF(x, y, refAltMatch = TRUE, mafObj = TRUE, ...)
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. |
subset table or an object of class MAF-class. If no overlaps found returns 'NULL'
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 variantsPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.