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

## rnb.execute.na.removal

### Description

Removes all probes with missing value (if such exists) from the given dataset.

### Usage

    rnb.execute.na.removal(
      rnb.set,
      threshold = rnb.getOption("filtering.missing.value.quantile")
    )

### Arguments

`rnb.set` | Methylation dataset as an object of type inheriting `RnBSet`.
`threshold` | Maximum quantile of `NA`s allowed per site. This must be a value between 0 and 1.

### Value

List of four or five elements:

`"dataset.before"`

  Copy of `rnb.set`.

`"dataset"`

  The (possibly modified) dataset after performing the missing value removal.

`"filtered"`

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

`"threshold"`

  Copy of `threshold`.

`"naCounts"`

  Vector storing the number of NAs per site

### Author(s)

Yassen Assenov

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    rnb.set.filtered <- rnb.execute.na.removal(rnb.set.example, 0)$dataset
    identical(meth(rnb.set.example), meth(rnb.set.filtered)) # TRUE

[Package RnBeads version 2.10.0 Index]