read_maf: Read MAF Files

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

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)

read_maf_minimal(dt)

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.
dt	A data.frame contains at least the following columns: "Tumor_Sample_Barcode", "Chromosome", "Start_Position", "End_Position", "Reference_Allele", "Tumor_Seq_Allele2"

Functions

• read_maf_minimal(): Read Maf data.frame from a minimal maf-like data

See Also

read_copynumber for reading copy number data to CopyNumber object.

Examples

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

  laml_mini <- laml@data[, list(
    Tumor_Sample_Barcode, Chromosome,
    Start_Position, End_Position,
    Reference_Allele, Tumor_Seq_Allele2
  )]
  laml2 <- read_maf_minimal(laml_mini)
  laml2
}

sigminer documentation built on Aug. 21, 2023, 9:08 a.m.