import_gff_gtf: Import .gtf and .gff files to be used during gene and QTL...

In GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

Import .gtf and .gff files to be used during gene and QTL annotation, respectively

Description

Takes a .gft or .gff file and import into a dataframe

Usage

import_gff_gtf(db_file, file_type)

Arguments

db_file	File with the gene mapping or QTL information. For gene mapping, a .gtf file from Ensembl database must be used. For the QTL search, a .gff file from Animal QTlLdb must be used. Both files must use the same reference annotation used in the original study
file_type	"gtf" or "gff"

Value

A dataframe with the gtf or gtf content

Examples

gffpath <- system.file("extdata", "example.gff", package="GALLO")

qtl.inp <- import_gff_gtf(db_file=gffpath,file_type="gff")

GALLO documentation built on June 22, 2024, 9:17 a.m.