sigminer (version 1.2.5)

read_maf: Read MAF Files

Description

This function is a wrapper of maftools::read.maf. Useless options in maftools::read.maf are dropped here. You can also use maftools::read.maf to read the data. All reference alleles and mutation alleles should be recorded in positive strand format.

Usage

read_maf(maf, verbose = TRUE)

Arguments

maf

tab delimited MAF file. File can also be gz compressed. Required. Alternatively, you can also provide already read MAF file as a dataframe.

verbose

TRUE logical. Default to be talkative and prints summary.

See Also

read_copynumber for reading copy number data to CopyNumber object.

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools", mustWork = TRUE)
if (!require("R.utils")) {
  message("Please install 'R.utils' package firstly")
} else {
  laml <- read_maf(maf = laml.maf)
  laml
}
# }