extendLeaders {ORFik} | R Documentation |
Will extend the leaders or transcripts upstream by extension.
Remember the extension is general not relative, that means splicing
will not be taken into account.
Requires the grl
to be sorted beforehand,
use sortPerGroup
to get sorted grl.
extendLeaders(grl, extension = 1000L, cds = NULL)
grl |
usually a |
extension |
an integer, how much to extend the leaders. Or a GRangesList where start / stops by strand are the positions to use as new starts. |
cds |
If you want to extend 5' leaders downstream, to catch upstream ORFs going into cds, include it. It will add first cds exon to grl matched by names. Do not add for transcripts, as they are already included. |
an extended GRangeslist
library(GenomicFeatures) samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package = "GenomicFeatures") txdb <- loadDb(samplefile) fiveUTRs <- fiveUTRsByTranscript(txdb) # <- extract only 5' leaders tx <- exonsBy(txdb, by = "tx", use.names = TRUE) cds <- cdsBy(txdb,"tx",use.names = TRUE) ## now try(extend upstream 1000, downstream 1st cds exons): extendLeaders(fiveUTRs, extension = 1000, cds) ## when extending transcripts, don't include cds' of course, ## since they are already there extendLeaders(tx, extension = 1000)