extendLeaders: Extend the leaders transcription start sites.
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value See Also Examples

Will extend the leaders or transcripts upstream (5' 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.

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

`grl`	usually a `GRangesList` of 5' utrs or transcripts. Can be used for any extension of groups.
`extension`	an integer, how much to extend upstream (5' 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 by strand are the positions to use as new starts.
`cds`	a `GRangesList` of coding sequences, If you want to extend 5' leaders downstream, to catch upstream ORFs going into cds, include it. It will add first cds exon to grl matched by names. Do not add for transcripts, as they are already included.
`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(), extendTrailers(), reduceKeepAttr(), tile1(), txSeqsFromFa(), windowPerGroup()

library(GenomicFeatures)
samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                          package = "GenomicFeatures")
txdb <- loadDb(samplefile)
fiveUTRs <- fiveUTRsByTranscript(txdb, use.names = TRUE) # <- extract only 5' leaders
tx <- exonsBy(txdb, by = "tx", use.names = TRUE)
cds <- cdsBy(txdb,"tx",use.names = TRUE)
## extend leaders upstream 1000
extendLeaders(fiveUTRs, extension = 1000)
## now try(extend upstream 1000, add all cds exons):
extendLeaders(fiveUTRs, extension = 1000, cds)

## when extending transcripts, don't include cds' of course,
## since they are already there
extendLeaders(tx, extension = 1000)
## Circular genome (allow negative coordinates)
circular_fives <- fiveUTRs
isCircular(circular_fives) <- rep(TRUE, length(isCircular(circular_fives)))
extendLeaders(circular_fives, extension = 32672841L)