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
BSrel object to these regions.
filterBySharedRegions(object, groups, perc.samples, no.samples, minCov)
OPTIONAL. A factor specifying two or more groups within the given object. See Details.
A numeric vector with elements between 0 and 1 of length 1 or of the same length as levels in group. Default is 1.
A numeric: If
group is given
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
perc.samples is given. Alternatively, the number of
samples can be given directly by using
1 2 3 4 5 6
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)
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