filterBySharedRegions: Reduces a 'BSraw' or 'BSrel' object to regions (or single...
In BiSeq: Processing and analyzing bisulfite sequencing data

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

This method determines the regions which are covered in a given fraction of samples and reduces the BSraw or BSrel object to these regions.

1	filterBySharedRegions(object, groups, perc.samples, no.samples, minCov)

`object`	A `BSraw` or `BSrel` object.
`groups`	OPTIONAL. A factor specifying two or more groups within the given object. See Details.
`perc.samples`	A numeric vector with elements between 0 and 1 of length 1 or of the same length as levels in group. Default is 1.
`no.samples`	Alternative to `perc.samples`. An integer vector of length 1 or of the same length as levels in group.
`minCov`	A numeric: If `object` is a `BSraw` object the minimum coverage may be set. Default is 1.

If argument group is given perc.samples or no.samples are applied for all group levels.

An object of the same class as object storing methylation information solely for regions or single CpGs covered in at least round(perc.samples*ncol(object)) samples, if perc.samples is given. Alternatively, the number of samples can be given directly by using no.samples.

Katja Hebestreit

filterByCov

data(rrbs)
rrbs.reduced <- filterBySharedRegions(object = rrbs, perc.samples = 1)

# Or filter CpG sites where at least 50% of cancer and 50% of normal samples have coverage:
rrbs.reduced <- filterBySharedRegions(object=rrbs, groups = colData(rrbs)$group,
                                      perc.samples = 0.5)