extendLeaders {ORFik} | R Documentation

## 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 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.
`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)

[Package ORFik version 1.10.13 Index]