loadRegion: Load transcript region

In ORFik: Open Reading Frames in Genomics

Description

Usefull to simplify loading of standard regions, like cds' and leaders.

Usage

loadRegion(txdb, part = "tx", names.keep = NULL, by = "tx")

Arguments

txdb	a TxDb file or a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite), if it is a GRangesList, it will return it self.
part	a character, one of: tx, leader, cds, trailer, intron, mrna NOTE: difference between tx and mrna is that tx are all transcripts, while mrna are all transcripts with a cds
names.keep	a character vector of subset of names to keep. Example: loadRegions(txdb, names = ENST1000005), will return only that transcript. Remember if you set by to "gene", then this list must be with gene names.
by	a character, default "tx" Either "tx" or "gene". What names to output region by, the transcript name "tx" or gene names "gene"

Details

Load as GRangesList if input is not already GRangesList.

Value

a GrangesList of region

Examples

gtf <- system.file("extdata", "annotations.gtf", package = "ORFik")
loadRegion(gtf, "cds")
loadRegion(gtf, "intron")

ORFik documentation built on March 27, 2021, 6 p.m.