extendTrailers {ORFik}R Documentation

Extend the Trailers transcription stop sites

Description

Will extend the trailers or transcripts downstream (3' end) 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 downstream (3' end). Eiter single value that will apply for all, or same as length of grl which will give 1 update value per grl object. Or a GRangesList where start / stops sites by strand are the positions to use as new starts.

Value

an extended GRangeslist

See Also

Other ExtendGenomicRanges: asTX(), coveragePerTiling(), extendLeaders(), reduceKeepAttr(), tile1(), txSeqsFromFa(), windowPerGroup()

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 1.8.6 Index]