replaceOutsideValues {BEclear} | R Documentation

## Replace DNA methylation values out of the boundaries

### Description

A method which replaces values below 0 or beyond 1 contained in the input matrix. These wrong entries are replaced by 0 or 1, respectively. Note that this method is especially designed for DNA methylation data.

### Usage

    replaceOutsideValues(data)

### Arguments

`data` | any matrix filled with values that normally should be bounded between 0 and 1.

### Details

replaceOutsideValues

Note that this method is especially designed to run after the batch effect correction of DNA methylation data, e.g. with the `imputeMissingData` method. It can happen, that the predicted values are lying slightly below the lower bound of 0 or beyond the upper bound of 1. This method finds these inaccurately predicted entries. Another method called `replaceOutsideValues` replaces these values either by 0 or 1, respectively. Another method called `findOutsideValues` returns a list of existing wrong values and can be run before the replacement.

### Value

Returns the input matrix with every value previously below 0 changed to 0 and every value previously beyond 1 changed to 1.

### See Also

`findOutsideValues`

`correctBatchEffect`

### Examples

    data(BEclearCorrected)
    # Replace wrongly predicted values
    corrected <- replaceOutsideValues(data = ex.corrected.data)

[Package BEclear version 2.6.0 Index]