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Read in a BED file and convert to GenomicRanges or data.table

Source: R/swissArmyKnife.R
read_bed_file.Rd

Read in a BED file and convert it to a GenomicRanges object or data.table with refactored seq details. Expects the first 3 columns as chromosome, start, end; However column names are not necessary. The BED file can be either zipped or unzipped.

Usage

read_bed_file(
  bed_file,
  output_type = c("gr", "dt"),
  has_header = FALSE,
  additional_col_names = NULL,
  cpus = 1,
  seq_lengths = gUtils::hg_seqlengths(),
  allow_nonstandard_chr = FALSE,
  verbose = TRUE
)

Arguments

bed_file

Path to BED file (supports .bed, .bed.gz)

output_type

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

has_header

Logical, does BED file have header line. Default: FALSE

additional_col_names

Character vector of names for additional columns in BED file, beyond first three. Default: NULL

cpus

Integer, number of CPUs for reading data, used by data.table::fread(). Default: 1

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"

allow_nonstandard_chr

Logical, whether to allow non-standard chromosomes (decoys, HLA, alt contigs). Default: FALSE

verbose

Logical, whether to print progress messages. Default: TRUE

Value

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