Man pages for uds-helms/BEclear
Correction of batch effects in DNA methylation data

BEclear-example-methylation-dataExample data set for the BEclear-package
BEclear-example-sample-dataExample data set for the BEclear-package
BEclear-packageCorrection of batch effects in DNA methylation data
calcBatchEffectsCalculate the Batch Effects in a given data set
calcBatchEffectsForBatchcalcBatchEffectsForBatch
calcBlockFramecalcBlockFrame
calcPositionscalcPositions
calcScorecalculate batch effect score
calcSummarySummarize median comparison and p-value calculation results
clearBEgenesPrepare a data matrix for the BEclear function
combineBlockscombineBlocks
correctBatchEffectCorrect a batch effect in DNA methylation data
countValuesToPredictCount NA entries in a matrix
ex.corrected.dataExample matrix of corrected data for the BEclear-package
findOutsideValuesFind DNA methylation values out of the boundaries
gdepochgdepoch
imputeMissingDataMatrix prediction using a Latent Factor Model
imputeMissingDataForBlockimputeMissingDataForBlock
localLossCalculating the Local Loss
lossloss
makeBoxplotproduce simple predefined boxplot for methylation data
preprocessBEclearpreprocessBEclear
replaceOutsideValuesReplace DNA methylation values out of the boundaries
runGradientDescentrunGradientDescent
uds-helms/BEclear documentation built on April 16, 2023, 12:44 a.m.