filter.hq.genes: Filter high quality genes

In jsalojar/PiNSiR: What the Package Does (One Line, Title Case)

Filter high quality genes

Description

This function selects high quality genes from the set of annotated genes in a given gff3 file. It checks that the gene length is divisible by three (so that codons are intact) and that the translated protein starts with a methionine.

Usage

filter.hq.genes(gff.file, peptide.fasta, bed = F, gene.identifier = "Parent")

Arguments

gff.file	Path to the input gff3 file with gene models.
peptide.fasta	Path to the input fasta file with protein sequences of the gene models.
bed	Logical, whether to return coordinates in a bed format (True; 0-based) or gff3 coordinates (False, default; starts from 1).
gene.identifier	The unique identifier for matching exons with gene models in the gff3 file. Default is "Parent"

Value

A list with two items: HQ - high quality gene models and ALL - all gene models. Each list item is a reduced gff3 file.

jsalojar/PiNSiR documentation built on Nov. 1, 2023, 1:47 p.m.