partitionRegions-methods {podkat} | R Documentation

## Partition Genomic Regions

### Description

Partitions genomic regions into windows of fixed size

### Usage

    ## S4 method for signature 'GRanges'
    partitionRegions(x, chrs=character(), width=5000, overlap=0.5)
    ## S4 method for signature 'GRangesList'
    partitionRegions(x, chrs=character(), width=5000, overlap=0.5)
    ## S4 method for signature 'MaskedBSgenome'
    partitionRegions(x, chrs=character(), width=5000, overlap=0.5, ...)

### Arguments

`x` | an object of class `GRanges`, `GRangesList`, or `MaskedBSgenome`
`chrs` | a character vector (possibly empty) with names of chromosomes to limit to
`width` | window size
`overlap` | amount of overlap; a zero value corresponds to non-overlapping windows and the default 0.5 corresponds to 50% overlap. The largest possible value is 0.8 which corresponds to an overlap of 80%.
`...` | further arguments are passed on to `unmaskedRegions`.

### Details

For a `GRanges` object `x`, this method partitions each genomic region into possibly overlapping, equally large windows of size `width`. The amount of overlap is controlled with the `overlap` parameter. The windows are placed such that possible overhangs are balanced at the beginning and end of the region. As an example, suppose we have a region from bases 1 to 14,000 and that we want to cover it with windows of 10,000bp length and 50% overlap. The straightforward approach would be to have two windows 1-10,000 and 5,001-15,000, and to crop the latter to 5,001-14,000. As said, the `partitionRegions` balances the overhangs, so it will return two windows 1-9,500 and 4,501-14,000 instead.

If `chrs` is not empty, `partitionRegions` will only consider regions from those chromosomes (i.e. regions in the `GRanges` object whose `seqnames` occur in `chrs`).

If called for a `GRangesList` object, all componentes of the `GRangesList` object are partitioned separately as described above.

For convenience, this function can also be called for a `MaskedBSgenome` object. In this case, `unmaskedRegions` is called before partitioning.

### Value

If `x` is a `GRanges` object, the function also returns a `GRanges` object. In the other two cases, a `GRangesList` object is returned.

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

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

### See Also

`assocTest`, `unmaskedRegions`, `unmasked-datasets`, `GRangesList`, `GRanges`

### Examples

    ## create a toy example
    gr <- GRanges(seqnames="chr1", ranges=IRanges(start=1, end=14000))
    partitionRegions(gr, width=10000, overlap=0.5)
    partitionRegions(gr, width=10000, overlap=0.8)
    partitionRegions(gr, width=10000, overlap=0)

    ## a toy example of a 'GRangesList'
    grL <- GRangesList(gr, GRanges(seqnames="chr2",
                                   ranges=IRanges(start=1, end=22000)))
    partitionRegions(grL, width=10000, overlap=0.5)
    partitionRegions(grL, width=10000, overlap=0.8)

    ## real-world example
    data(hg38Unmasked)
    partitionRegions(hg38Unmasked, chrs="chr22", width=20000)

[Package podkat version 1.12.0 Index]