extendTrailers {ORFik} | R Documentation

## Extend the Trailers transcription stop sites

### Description

Will extend the trailers or transcripts downstream 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

    extendTrailers(grl, extension = 1000L)

### Arguments

`grl` | usually a `GRangesList` of 3' 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.

### Value

an extended GRangeslist

### 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)

[Package ORFik version 1.6.9 Index]