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

[Package RnBeads version 2.10.0 Index]