compEpiTools (version 1.6.3)

countOverlapsInBins-methods: given a query and a subject GRanges returns a matrix of counts of subject in bins of query

Description

Given a query and a subject GRanges, this function returns a matrix with number of rows equal to the number of regions in query and number of columns equal to the number of bins. For each bin of each region, the occurrence (1) or not (0) of subject is returned.

Methods

The countOverlaps method can be used to determine the overlap between a query and a subject GRanges. The countOverlapsInBins method add the functionality to partition query in bins. To be used in this form: countOverlapsInBins(query, subject, nbins) where:

• query: GRanges
• subject: GRanges
• nbins: numeric, the number of bins

It returns a matrix with number of rows equal to the number of regions in query and number of columns equal to the number of bins. For each bin of each region 1 is assigned of subject GRanges overlap, 0 if it does not.

Examples

gr1 <- GRanges(seqnames=Rle('chr1',2), ranges=IRanges(start=c(10,100), end=c(50, 150)))
gr2 <- GRanges(seqnames=Rle('chr1',2), ranges=IRanges(start=c(2,40), end=c(15, 70)))
countOverlapsInBins(gr1, gr2, nbins=4)