extendLeaders {ORFik}R Documentation

Extend the leaders transcription start sites.

Description

Will extend the leaders or transcripts upstream 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

extendLeaders(grl, extension = 1000L, cds = NULL)

Arguments

grl

usually a GRangesList of 5' utrs or transcripts. Can be used for any extension of groups.

extension

an integer, how much to extend the leaders. Or a GRangesList where start / stops by strand are the positions to use as new starts.

cds

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.

Value

an extended GRangeslist

Examples

library(GenomicFeatures)
samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                          package = "GenomicFeatures")
txdb <- loadDb(samplefile)
fiveUTRs <- fiveUTRsByTranscript(txdb) # <- extract only 5' leaders
tx <- exonsBy(txdb, by = "tx", use.names = TRUE)
cds <- cdsBy(txdb,"tx",use.names = TRUE)
## now try(extend upstream 1000, downstream 1st 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)


[Package ORFik version 1.4.0 Index]