get_cdsgrl: Get a set of filtered cds from an imported GTF GRanges
In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

get_cdsgrl

R Documentation

Get a set of filtered cds from an imported GTF GRanges

Description

Get a set of filtered cds from an imported GTF GRanges

Usage

get_cdsgrl(filt_anno, fafileob, ignore_orf_validity)

Arguments

`filt_anno`	GRanges; an unfilted imported GTF
`fafileob`	FaFile object; reference to an indexed genomic fasta file
`ignore_orf_validity`	Boolean; flag whether to include ORFs missing a valid stop codon

Details

This takes only coding sequences which are a multiple of 3bp and have a start and a stop on either end.it always returns coding sequences without the stops, regardless of their extent in the input.