extendLeaders: Extend the leaders transcription start sites.

In JokingHero/ORFik: Open Reading Frames in Genomics

Extend the leaders transcription start sites.

Description

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.

Usage

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

Arguments

grl	usually a GRangesList of 5' utrs or transcripts. Can be used for any extension of groups.
extension	an integer, how much to max extend upstream (5' 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 by strand are the positions to use as new starts. Will not cross the chromosome boundary for non circular chromosomes.
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.

Value

an extended GRangeslist

See Also

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

Examples

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)

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