loadRegion {ORFik} | R Documentation

## Load transcript region

### 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")

[Package ORFik version 1.10.13 Index]