podkat (version 1.4.2)

split-methods: Split GRanges Object

Description

Splits a GRanges object into a GRangesList

Usage

## S3 method for class 'GRanges,GRangesList':
split(x, f)

Arguments

x

object of class GRanges

f

object of class GRangesList

Value

• a GRangesList object (see details above)

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.

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")])
}