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