Number of methylated and unmethylated reads
of a CpG site with coverage above
maxCov are reduced such that
the methylation level remains unchanged.
The maximum number of reads a CpG should have. All coverages above this threshold are limited. (Default is 50)
This function might be useful prior to the use of
predictMeth to limit the weights of CpGs with extremly
high coverages. See
binomLikelihoodSmooth for details.
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data(rrbs) rrbs.clust.unlim <- clusterSites(object = rrbs, groups = colData(rrbs)$group, perc.samples = 4/5, min.sites = 20, max.dist = 100) covBoxplots(rrbs.clust.unlim) # 90% quantile of coverage is 39x quantile(totalReads(rrbs.clust.unlim)[totalReads(rrbs.clust.unlim)>0], 0.9) rrbs.clust.lim <- limitCov(rrbs.clust.unlim, maxCov = 39) covBoxplots(rrbs.clust.lim)
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