BEclear (version 1.4.0)

findWrongValues: Find DNA methylation values out of the boundaries

Description

A method which lists values below 0 or beyond 1 contained in the input matrix. The wrong entries are stored in a data.frame together with the corresponding row and column position of the matrix. Note that this method is especially designed for DNA methylation data.

Usage

findWrongValues(data)

Arguments

data

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

Value

A data frame containing the columns "level", "row", "col" and "value" defining if the wrong value is below 0 or beyond 1 (level = 0 or level = 1), the row position and the column position in the input matrix and the wrong value itself, respectively.

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.

See Also

BEclear replaceWrongValues correctBatchEffect

Examples

data(BEclearCorrected)
# Find wrongly predicted values
wrongEntries <- findWrongValues(data=ex.corrected.data)