replaceOutsideValues: Replace DNA methylation values out of the boundaries

In David-J-R/BEclear: Correction of batch effects in DNA methylation data

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)

David-J-R/BEclear documentation built on April 17, 2023, 2:19 p.m.