split-methods {podkat} | R Documentation

## Split `GRanges` Object

### Description

Splits a `GRanges` object into a `GRangesList`

### Usage

    ## S4 method for signature 'GRanges,GRangesList'
    split(x, f)

### Arguments

`x` | object of class `GRanges`
`f` | object of class `GRangesList`

### Details

This function splits a `GRanges` object `x` along a `GRangesList` object `f`. More specifically, each region in `x` is checked for overlaps with every list component of `f`. The function returns a `GRangesList` object each component of which contains all overlaps of `x` with one of the components of `f`. If the overlap is empty, this component is discarded.

This function is mainly made for splitting regions of interests (transcripts, exons, regions targeted by exome capturing) along chromosomes (and pseudoautosomal regions).

The returned object inherits sequence infos (chromosome names, chromosome lengths, genome, etc.) from the `GRangesList` object `f`.

For greater universality, the function takes strand information into account. If overlaps should not be determined in a strand-specific manner, all strand information must be discarded from `x` and `f` before calling `split`.

### Value

a `GRangesList` object (see details above)

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

http://www.bioinf.jku.at/software/podkat

### See Also

`GRanges`, `GRangesList`

### Examples

    ## set up toy example
    chr1 <- GRanges(seqnames="chr1", ranges=IRanges(start=1, end=200000))
    chr2 <- GRanges(seqnames="chr2", ranges=IRanges(start=1, end=180000))
    grL <- GRangesList(list(chr1=chr1, chr2=chr2))
    seqlevels(grL) <- c("chr1", "chr2")
    seqlengths(grL) <- c(chr1=200000, chr2=180000)
    grL

    ## split set of regions given as 'GRanges' object
    gr <- GRanges(seqnames=c("chr1", "chr1", "chr2", "chr2", "chr2"),
                  ranges=IRanges(start=c(1, 30000, 10000, 51000, 110000),
                                 end=c(340, 37000, 10100, 61000, 176000)))
    gr
    split(gr, grL)

    ## consider transcripts on the X chromosome, but with pseudoautosomal
    ## regions treated separately
    if (require(TxDb.Hsapiens.UCSC.hg38.knownGene))
    {
        data(hg38Unmasked)

        hg38tr <- transcripts(TxDb.Hsapiens.UCSC.hg38.knownGene)
        strand(hg38tr) <- "*"

        split(hg38tr, hg38Unmasked[c("chrX", "X.PAR1", "X.PAR2", "X.XTR")])
    }

[Package podkat version 1.14.0 Index]