extendTrailers: Extend the Trailers transcription stop sites
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value See Also Examples

Will extend the trailers or transcripts downstream (3' end) by extension. 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,
  is.circular = all(isCircular(grl) %in% TRUE)
)

`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.
`is.circular`	logical, default FALSE if not any is: all(isCircular(grl) Where grl is the ranges checked. If TRUE, allow ranges to extend below position 1 on chromosome. Since circular genomes can have negative coordinates.

an extended GRangeslist

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

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)
## Circular genome (allow negative coordinates)
circular_three <- threeUTRs
isCircular(circular_three) <- rep(TRUE, length(isCircular(circular_three)))
extendTrailers(circular_three, extension = 126200008L)[41] # <- negative stop coordinate