computeOverlapProfile {DMRcaller}

R Documentation

Compute Overlaps Profile

Description

This function computes the distribution of a subset of regions (GRanges object) over a large region (GRanges object)

Usage

computeOverlapProfile(subRegions, largeRegion,
  windowSize = floor(width(largeRegion)/500), binary = TRUE, cores = 1)

Arguments

subRegions	a GRanges object with the sub regions; e.g. can be the DMRs.
largeRegion	a GRanges object with the region where to compute the overlaps; e.g. a chromosome
windowSize	The largeRegion is partitioned into equal sized tiles of width windowSize.
binary	a value indicating whether to count 1 for each overlap or to compute the width of the overlap
cores	the number of cores used to compute the DMRs.

Value

a 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.

Author(s)

Nicolae Radu Zabet

See Also

plotOverlapProfile, filterDMRs, computeDMRs and mergeDMRsIteratively

Examples

# 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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