computeOverlapProfile {DMRcaller} | R Documentation |
This function computes the distribution of a subset of regions
(GRanges
object) over a large region (GRanges
object)
computeOverlapProfile(subRegions, largeRegion, windowSize = floor(width(largeRegion)/500), binary = TRUE, cores = 1)
subRegions |
a |
largeRegion |
a |
windowSize |
The |
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. |
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
.
Nicolae Radu Zabet
plotOverlapProfile
, filterDMRs
,
computeDMRs
and mergeDMRsIteratively
# 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)