extendTrailers: Extend the Trailers transcription stop sites

In JokingHero/ORFik: Open Reading Frames in Genomics

Extend the Trailers transcription stop sites

Description

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.

Usage

extendTrailers(
  grl,
  extension = 1000L,
  is.circular = all(isCircular(grl) %in% TRUE)
)

Arguments

grl	usually a GRangesList of 3' utrs or transcripts. Can be used for any extension of groups.
extension	an integer, how much to max extend downstream (3' end). Either 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. Will not cross the chromosome boundary for non circular chromosomes.
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.

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)
## 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

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.