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Read MAF file and convert to GenomicRanges or data.table

Source: R/swissArmyKnife.R
read_maf_file.Rd

Read in a MAF file which contains a number of columns and convert it to a GenomicRanges object or data.table. The MAF file can be either zipped or unzipped. This function performs validation and filtering to ensure proper MAF format compliance. For more specific MAFtools operations, see maftools::read.maf()

Usage

read_maf_file(
  maf_file,
  output_type = c("gr", "dt"),
  cpus = 2,
  seq_lengths = gUtils::hg_seqlengths(),
  verbose = TRUE
)

Arguments

maf_file

Path to MAF file (supports .maf, .maf.gz, .maf.txt, .txt)

output_type

Character string specifying output format: gr="GenomicRanges" (default) or dt="data.table"

cpus

Number of CPUs for reading data, used by data.table::fread(). Default: 2

seq_lengths

Named vector object used as template for new seq details. See gUtils::hg_seqlengths() for example. Default: hg38 seqlengths. Only used when output_type = "GenomicRanges"

verbose

Logical, whether to print progress messages. Default: TRUE

Value

GenomicRanges object or data.table with MAF data. If GenomicRanges, includes updated seqinfo, seqnames, seqlengths, seqlevels