loadRegions {ORFik} | R Documentation

## 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 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.
`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"))

[Package ORFik version 1.14.7 Index]