loadRegions: Get all regions of transcripts specified to environment

In JokingHero/ORFik: Open Reading Frames in Genomics

Get all regions of transcripts specified to environment

Description

By default loads all parts to .GlobalEnv (global environemnt) Useful to not spend time on finding the functions to load regions.

Usage

loadRegions(
  txdb,
  parts = c("mrna", "leaders", "cds", "trailers"),
  extension = "",
  names.keep = NULL,
  by = "tx",
  skip.optimized = FALSE,
  envir = .GlobalEnv
)

Arguments

txdb	a TxDb file, a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite) or an ORFik experiment
parts	the transcript parts you want, default: c("mrna", "leaders", "cds", "trailers"). See ?loadRegion for more info on this argument.
extension	What to add on the name after leader, like: B -> leadersB
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.
envir	Which environment to save to, default: .GlobalEnv

Value

invisible(NULL) (regions saved in envir)

Examples

# Load all mrna regions to Global environment
gtf <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                        package = "GenomicFeatures")
loadRegions(gtf, parts = c("mrna", "leaders", "cds", "trailers"))

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