extendTrailers {ORFik} | R Documentation

## Extend the Trailers transcription stop sites

### Description

Will extend the trailers or transcripts downstream (3' 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

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

### 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 downstream (3' 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 sites by strand are the positions to use as new starts.
`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()`, `extendLeaders()`, `reduceKeepAttr()`, `tile1()`, `txSeqsFromFa()`, `windowPerGroup()`

### 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)
    ## Circular genome (allow negative coordinates)
    circular_three <- threeUTRs
    isCircular(circular_three) <- rep(TRUE, length(isCircular(circular_three)))
    extendTrailers(circular_three, extension = 126200008L)[41] # <- negative stop coordinate

[Package ORFik version 1.12.13 Index]