limitCov: Limits the coverage of a 'BSraw' object
In BiSeq: Processing and analyzing bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also Examples

Number of methylated and unmethylated reads of a CpG site with coverage above maxCov are reduced such that the methylation level remains unchanged.

1	limitCov(object, maxCov)

`object`	A `BSraw`.
`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)