maftools (version 0.99.30)

read.maf: Read MAF files.

Description

Takes tab delimited MAF (can be plain text or gz compressed) file as an input and summarizes it in various ways. Also creates oncomatrix - helpful for visualization.

Usage

read.maf(maf, removeSilent = TRUE, useAll = FALSE)

Arguments

maf

tab delimited MAF file. File can also be gz compressed.

removeSilent

logical. Whether to discard silent (with no functional impact) mutations ("Silent","Intron","RNA","3'UTR"). Default is TRUE.

useAll

logical. Whether to use all variants irrespective of values in Mutation_Status. Defaults to False. Only uses with values Somatic.

Value

An object of class MAF.

See Also

plotmafSummary write.mafSummary

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
# }