loadRegion {ORFik} | R Documentation

## Load transcript region

### Description

Usefull to simplify loading of standard regions, like cds' and leaders. Adds another safety in that seqlevels will be set

### Usage

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

### 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, ncRNA, mrna, leader, cds, trailer, intron, NOTE: difference between tx and mrna is that tx are all transcripts, while mrna are all transcripts with a cds, respectivly ncRNA are all tx without 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". NOTE: this is note the same as cdsBy(txdb, by = "gene"), cdsBy would then only give 1 cds per Gene, loadRegion gives all isoforms, but with gene names.
`skip.optimized` | logical, default FALSE. If TRUE, will not search for optimized rds files to load created from ORFik::makeTxdbFromGenome(..., optimize = TRUE). The optimized files are ~ 100x faster to load for human genome.

### Details

Load as GRangesList if input is not already GRangesList.

### Value

a GrangesList of region

### Examples

    gtf <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                            package = "GenomicFeatures")
    loadRegion(gtf, "cds")
    loadRegion(gtf, "intron")

[Package ORFik version 1.14.7 Index]