get_cdsgrl: Get a set of filtered cds from an imported GTF GRanges

get_cdsgrlR 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.

Value

a GRangesList split by transcript, which contains the filtered coding ranges for each one

Author(s)

Dermot Harnett, dermot.p.harnett@gmail.com


zslastman/RiboStan documentation built on June 12, 2024, 1:59 a.m.