Import intervals from a GFF/GTF file

Reads a GFF3 or GTF file (optionally gzipped) and returns a misha 1D intervals data frame. GFF/GTF are 1-based and inclusive on both ends; coordinates are converted to 0-based half-open by subtracting 1 from start and leaving end as-is.

Usage

gintervals.import_gff(file = NULL, feature = NULL, strand = TRUE, attrs = TRUE)

Arguments

file

path to a GFF/GTF file.

feature

optional feature-type filter (column 3 of GFF). Pass a character vector to keep only those types (e.g. "exon", c("gene", "transcript")).

strand

if TRUE, include the strand column.

attrs

if TRUE, include the raw attributes string as column attrs. The attribute string is not parsed.

Value

A 1D intervals data frame with columns chrom, start, end, and optionally strand, type, source, score, attrs.

Details

Chromosome names are normalized through the active database's CHROM_ALIAS mechanism.

See also

gintervals.import_bed, gintervals.import_vcf.