findOutsideValues: Find DNA methylation values out of the boundaries

In BEclear: Correction of batch effects in DNA methylation data

Description

A method which lists values below 0 or beyond 1 contained in the input matrix. These 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

findOutsideValues(data)

Arguments

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

Details

findOutsideValues

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 replaceOutsideValues replaces these values either by 0 or 1, respectively.

Value

A data frame containing the columns "level", "row", "col" and "value" defining if the 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 value itself, respectively.

See Also

replaceOutsideValues

correctBatchEffect

Examples

data(BEclearCorrected)
# Find predicted values outside of the boundaries
outsideEntries <- findOutsideValues(data = ex.corrected.data)

BEclear documentation built on Nov. 8, 2020, 8:07 p.m.