rnb.execute.high.dpval.masking {RnBeads}

R Documentation

rnb.execute.high.dpval.masking

Description

Replaces all low coverage sites by NA.

Usage

rnb.execute.high.dpval.masking(rnb.set, dpval.threshold = 0.05)

Arguments

rnb.set	Methylation dataset as an object of type inheriting RnBeadSet.
dpval.threshold	Threshold for maximal acceptable detection p-value, given as a non-negative numeric value between 0 and 1. All methylation measurements with detection p-value 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

Author(s)

Fabian Mueller

---