R: Extend the leaders transcription start sites.

extendLeaders {ORFik}

R Documentation

Extend the leaders transcription start sites.

Description

Will extend the leaders or transcripts upstream (5' end) 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 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.

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)