extendTrailers {ORFik} | R Documentation |
Will extend the trailers or transcripts downstream 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.
extendTrailers(grl, extension = 1000L)
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. |
an extended GRangeslist
library(GenomicFeatures) samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package = "GenomicFeatures") txdb <- loadDb(samplefile) threeUTRs <- threeUTRsByTranscript(txdb) # <- extract only 5' leaders tx <- exonsBy(txdb, by = "tx", use.names = TRUE) ## now try(extend downstream 1000): extendTrailers(threeUTRs, extension = 1000) ## Or on transcripts extendTrailers(tx, extension = 1000)