rnb.execute.low.coverage.masking {RnBeads} | R Documentation

## 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

### Author(s)

Fabian Mueller

[Package RnBeads version 2.0.1 Index]