podkat (version 1.4.2)

partitionRegions-methods: Partition Genomic Regions

Description

Partitions genomic regions into windows of fixed size

Usage

## S3 method for class 'GRanges':
partitionRegions(x, chrs=character(), width=5000, overlap=0.5)
## S3 method for class 'GRangesList':
partitionRegions(x, chrs=character(), width=5000, overlap=0.5)
## S3 method for class '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.

Value

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

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.

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)