loadRegions: Get all regions of transcripts specified to environment
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value Examples

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

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

`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"
`envir`	Which environment to save to, default: .GlobalEnv

invisible(NULL) (regions saved in envir)

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