loadRegion: Load transcript region

In JokingHero/ORFik: Open Reading Frames in Genomics

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")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.