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Import intervals from a BED file

Source: R/intervals-import.R
gintervals.import_bed.Rd

Reads a BED file, plain or gzipped, and returns a misha 1D intervals data frame. Track/browser/comment header lines are skipped automatically. Chromosome names are normalized through the active database's CHROM_ALIAS mechanism (so chr1 <-> 1 works without explicit configuration).

Usage

gintervals.import_bed(file = NULL, name = TRUE, score = TRUE, strand = TRUE)

Arguments

file

path to a BED file (.bed or .bed.gz). Zip archives are not supported - unzip them first.

name

if TRUE and a 4th column exists, include it as name.

score

if TRUE and a 5th (numeric) column exists, include it as score.

strand

if TRUE and a 6th column exists, include it as strand (mapped to 1/-1/0).

Value

A 1D intervals data frame, sorted by chrom and start.

Details

BED is already 0-based half-open, so coordinates are taken as-is.

See also

gintervals.import_gff, gintervals.import_vcf.