Partitions genomic regions into windows of fixed size
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## 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, ...)
an object of class
a character vector (possibly empty) with names of chromosomes to limit to
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
x, this method
partitions each genomic region into possibly overlapping, equally large
windows of size
width. The amount of overlap is controlled with
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
chrs is not empty,
partitionRegions will only
consider regions from those chromosomes (i.e. regions in the
GRanges object whose
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
MaskedBSgenome object. In this case,
unmaskedRegions is called before partitioning.
x is a
GRanges object, the function
also returns a
GRanges object. In the other two
GRangesList object is returned.
Ulrich Bodenhofer email@example.com
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## 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)
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