Compute Overlaps Profile
This function computes the distribution of a subset of regions
GRanges object) over a large region (
a value indicating whether to count 1 for each overlap or to compute the width of the overlap
the number of cores used to compute the DMRs.
GRanges object with equal sized tiles of the regions.
The object has one metadata file
score which represents: the number of
subRegions overlapping with the tile, in the case of
binary = TRUE,
and the width of the subRegions overlapping with the tile , in the case of
binary = FALSE.
Nicolae Radu Zabet
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# load the methylation data data(methylationDataList) # load the DMRs in CG context data(DMRsNoiseFilterCG) # the coordinates of the area to be plotted largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5)) # compute overlaps distribution hotspots <- computeOverlapProfile(DMRsNoiseFilterCG, largeRegion, windowSize = 10000, binary = FALSE)
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