limitCov {BiSeq} | R Documentation |
BSraw
objectNumber of methylated and unmethylated reads
of a CpG site with coverage above maxCov
are reduced such that
the methylation level remains unchanged.
limitCov(object, maxCov)
object |
A |
maxCov |
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.
A BSraw
object.
Katja Hebestreit
predictMeth
, binomLikelihoodSmooth
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)