maftools: filterMaf – R documentation

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filterMaf

Filter MAF objects

Description

Filter MAF by genes or samples

Usage

filterMaf(maf, genes = NULL, tsb = NULL, isTCGA = FALSE)

Arguments

`maf`	an MAF object generated by `read.maf`
`genes`	remove these genes
`tsb`	remove these samples (Tumor Sample Barcodes)
`isTCGA`	FALSE

Value

Filtered object of class MAF-class

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
#get rid of samples of interest
filterMaf(maf = laml, tsb = c("TCGA-AB-2830", "TCGA-AB-2804"))
#remove genes of intrest
filterMaf(maf = laml, genes =c("TTN", "AHNAK2"))

maftools

Summarize, Analyze and Visualize MAF Files

v2.6.05

MIT + file LICENSE

Authors

Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)

Initial release

2015-12-14