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.
read_maf(maf, verbose = TRUE)
maf | tab delimited MAF file. File can also be gz compressed. Required. Alternatively, you can also provide already read MAF file as a dataframe. |
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verbose | TRUE logical. Default to be talkative and prints summary. |
read_copynumber for reading copy number data to CopyNumber object.
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 }