BEclear (version 1.4.0)

Correct for batch effects in DNA methylation data

Description

Provides some functions to detect and correct for batch effects in DNA methylation data. The core function "BEclear" is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

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Version

1.4.0

License

GPL-2

Maintainer

Markus Merl

Last Published

February 15th, 2017

Functions in BEclear (1.4.0)

BEclear-package

Correct for batch effects in DNA methylation data

calcPvalues

Calculate p-values

clearBEgenes

Prepare a data matrix for the BEclear function

countValuesToPredict

Count NA entries in a matrix

BEclear

Matrix prediction method using a Latent Factor Model

ex.corrected.data

Example matrix of corrected data for the BEclear-package

calcScore

calculate batch effect score

calcSummary

Summarize median comparison and p-value calculation results

findWrongValues

Find DNA methylation values out of the boundaries

correctBatchEffect

Correct a batch effect in DNA methylation data

makeBoxplot

produce simple predefined boxplot for methylation data

replaceWrongValues

Replace DNA methylation values out of the boundaries

BEclear example data

Example data set for the BEclear-package

calcMedians

Calculate median difference values