extendTrailers {ORFik}R Documentation

Extend the Trailers transcription stop sites

Description

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.

Usage

extendTrailers(grl, extension = 1000L)

Arguments

grl

usually a GRangesList of 3' utrs or transcripts. Can be used for any extension of groups.

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.

Value

an extended GRangeslist

Examples

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)


[Package ORFik version 1.6.9 Index]