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, 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". 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", "annotations.gtf", package = "ORFik")
loadRegion(gtf, "cds")
loadRegion(gtf, "intron")

[Package ORFik version 1.13.14 Index]