loadRegion: Load transcript region
In Roleren/ORFik: Open Reading Frames in Genomics

loadRegion

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 object, ORFik experiment object or a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite), Only in the loadRegion function: 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 not 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 file is slow, but possible to use
gtf <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                        package = "GenomicFeatures")
txdb <- loadTxdb(gtf)
loadRegion(txdb, "cds")
loadRegion(txdb, "intron")
# Use txdb from experiment
df <- ORFik.template.experiment()
txdb <- loadTxdb(df)
loadRegion(txdb, "leaders")
# Use ORFik experiment directly
loadRegion(df, "mrna")

Roleren/ORFik documentation built on Dec. 18, 2024, 11:39 p.m.