Description Usage Arguments Details Value Author(s) See Also Examples
This method summarizes the methylation states of single CpG sites to a single methylation state for a given genomic region.
summarizeRegions(object, regions, outputAll)
A logical. If
When the given object is of class
(methylated) reads of all CpG site lying within a region are summed up and
assign as total number of (methylated) reads to that region. It is recommended
limitCov before applying
summarizeRegions to an
BSraw-class object in order to avoid an excessive influence of a
single CpG site on the methylation value of a region. When the
given object is of class
BSrel-class, the mean relative methylation
of all CpGs within a region is assign to that region.
rowRanges slot of the returned object is the given object
regions with all columns preserved.
BSraw or an
BSrel object storing methylation information about
the given regions.
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data(rrbs) rrbs.clustered <- clusterSites(rrbs) regions <- clusterSitesToGR(rrbs.clustered) rrbs <- limitCov(rrbs, maxCov=50) rrbsRegion <- summarizeRegions(rrbs, regions) totalReads(rrbsRegion)
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