BEclear (version 1.4.0)

replaceWrongValues: 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

replaceWrongValues(data)

Arguments

data

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

Value

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

Details

Note that this method is especially designed to run after the batch effect correction of DNA methylation data, e.g. with the BEclear 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 replaceWrongValues replaces these values either by 0 or 1, respectively. Another method called findWrongValues returns a list of existing wrong values and can be run before the replacement.

See Also

BEclear findWrongValues correctBatchEffect

Examples

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