# Correction of batch effects in DNA methylation data

## Documentation for package ‘BEclear’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BEclear-package | Correction of batch effects in DNA methylation data
BEclear | Example data set for the BEclear-package
BEclear example methylation data | Example data set for the BEclear-package
BEclear example sample data | Example data set for the BEclear-package
BEclearData | Example data set for the BEclear-package
calcBatchEffects | Calculate the Batch Effects in a given data set
calcScore | calculate batch effect score
calcSummary | Summarize median comparison and p-value calculation results
clearBEgenes | Prepare a data matrix for the BEclear function
correctBatchEffect | Correct a batch effect in DNA methylation data
countValuesToPredict | Count NA entries in a matrix
data | Example data set for the BEclear-package
ex.corrected.data | Example matrix of corrected data for the BEclear-package
ex.data | Example data set for the BEclear-package
ex.samples | Example data set for the BEclear-package
example | Example data set for the BEclear-package
findOutsideValues | Find DNA methylation values out of the boundaries
imputeMissingData | Matrix prediction method using a Latent Factor Model
loss | loss
makeBoxplot | produce simple predefined boxplot for methylation data
methylation | Example data set for the BEclear-package
preprocessBEclear | preprocessBEclear
replaceOutsideValues | Replace DNA methylation values out of the boundaries
_PACKAGE | Correction of batch effects in DNA methylation data