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)

[Package DMRcaller version 1.12.7 Index]