RnBeads (version 1.4.0)

rnb.execute.low.coverage.masking: rnb.execute.low.coverage.masking

Description

Replaces all low coverage sites by NA.

Usage

rnb.execute.low.coverage.masking(rnb.set, covg.threshold = rnb.getOption("filtering.coverage.threshold"))

Arguments

rnb.set

Methylation dataset as an object of type inheriting RnBSet.

covg.threshold

Threshold for minimal acceptable coverage, given as a non-negative integer value. All methylation measurements with lower coverage than this threshold are set to NA. If this parameter is 0, calling this method has no effect.

Value

List of three elements:

"dataset.before"

Copy of rnb.set.

"dataset"

The (possibly) modified dataset after retaining sites on autosomes only.

"mask"

A logical matrix of dimension meth(rnb.set,type="sites") indicating which methylation values have been masked