Correct for batch effects in DNA methylation data


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Documentation for package ‘BEclear’ version 1.14.0

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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
calcMedians Calculate median difference values
calcPvalues Calculate p-values
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
findWrongValues Find DNA methylation values out of the boundaries
imputeMissingData Matrix prediction method using a Latent Factor Model
makeBoxplot produce simple predefined boxplot for methylation data
methylation Example data set for the BEclear-package
replaceWrongValues Replace DNA methylation values out of the boundaries
_PACKAGE Correction of batch effects in DNA methylation data