filterMaf: Filter MAF objects
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

filterMaf

R Documentation

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"))

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.