intersect_bed: Extract gtf coordinates intersecting input bed file

In openanalytics/gread: Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Description

Given a gtf file, and a bed file, this function extracts all transcripts that overlap with coordinates from bed file and returns a filtered gtf file. This function is at the moment only for internal purposes.

Usage

intersect_bed(gtf_file, bed_file, select_features)

Arguments

gtf_file	Full path to a gtf file.
bed_file	Full path to a bed file. The file must contain at least three columns, with them corresponding to seqnames (or chr), start and end.
select_features	A 1-column data.table or a named list of length=1. The name of the list indicates the column in the gtf file to filter on. The column/value should be a character vector containing the values to retain.

Value

A gtf object that inherits from GRanges containing just those transcripts that overlap with the provided bed file.

See Also

read_format, non_overlaps, construct_introns, extract

openanalytics/gread documentation built on May 24, 2019, 2:29 p.m.