R: Filters regions (or single CpGs) of a 'BSraw' object with a...

filterByCov {BiSeq}

R Documentation

Filters regions (or single CpGs) of a `BSraw` object with a minimum coverage

This method reduces a BSraw object to its regions (or single CpGs) with a minimum number of reads.

filterByCov(object, minCov, global)

`object`	A `BSraw`.
`minCov`	Minimum number of reads overlapping the CpG sites.
`global`	A logical indicating whether the regions should achieve the minimum coverage in each sample. If `global = TRUE` the filtered object will consist of the regions achieving the minimum coverage in all samples. If `global = FALSE` (default) this function filters the regions for each sample separately, irrespectively of the coverages in other samples. `totalReads` and `methReads` are set to zero, if the minimum coverage is not obtained. Regions covered too sparse in all samples are dropped.

A BSraw object containing the CpGs or regions achieving the minimum coverage in all (if global=TRUE) or at least one (if global=FALSE) samples.

Katja Hebestreit

data(rrbs)
rrbs.reduced <- filterByCov(object=rrbs, minCov=10, global=TRUE)

[Package BiSeq version 1.22.0 Index]