gintervals.import_bed: Import intervals from a BED file

In misha: Toolkit for Analysis of Genomic Data

Import intervals from a BED file

Description

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).

Details

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

Value

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

See Also

gintervals.import_gff, gintervals.import_vcf.

misha documentation built on Aug. 24, 2026, 5:14 p.m.