object into regional counts for a given
a GRanges or GRangesList object.
number minimum bases covered per region (Default:0). Only regions with base coverage above this threshold are returned.
if set to TRUE only CpGs that match the strand of the region will be summarized. (default:FALSE)
a new methylRaw,methylBase or methylRawList object. If
strand.aware is set to FALSE (default). Even
though the resulting object will have the strand
regions it will still contain
methylation information from both strands.
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data(methylKit) # get the windows of interest as a GRanges object, this can be any set # of genomic locations library(GenomicRanges) my.win=GRanges(seqnames="chr21", ranges=IRanges(start=seq(from=9764513,by=10000,length.out=20),width=5000) ) # getting counts per region regional.methylRaw=regionCounts(object=methylRawList.obj, regions=my.win, cov.bases=0,strand.aware=FALSE)
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