rnb.execute.variability.removal {RnBeads} | R Documentation

## rnb.execute.variability.removal

### Description

Removes all sites or probes with low variability from the given dataset.

### Usage

    rnb.execute.variability.removal(
      rnb.set,
      min.deviation = rnb.getOption("filtering.deviation.threshold")
    )

### Arguments

`rnb.set` | Methylation dataset as an object of type inheriting `RnBSet`.
`min.deviation` | Threshold for standard deviation per site. This must be a scalar between 0 and 1. All sites, for which the standard deviation of methylation values (for all samples in `rnb.set`) is lower than this threshold, will be filtered out.

### Value

List of four elements:

`"dataset.before"`

  Copy of `rnb.set`.

`"dataset"`

  The (possibly modified) dataset after removing sites with low variability.

`"filtered"`

  `integer` vector storing the indices (in beta matrix of the unfiltered dataset) of all removed sites.

`"threshold"`

  The value of the given parameter `min.deviation`.

### Author(s)

Yassen Assenov

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    rnb.set.filtered <- rnb.execute.variability.removal(rnb.set.example, 0.01)

[Package RnBeads version 2.10.0 Index]