## 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, ...)GRanges GRangesList MaskedBSgenomeunmaskedRegions.x is a GRanges GRanges GRangesList GRanges 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 seqnames occur
in chrs). If called for a
For convenience, this function can also be called
for a MaskedBSgenome object. In this case,
unmaskedRegions is called before partitioning.
assocTest, unmaskedRegions,
unmasked-datasets, GRangesList GRanges ## 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)Run the code above in your browser using DataLab