Man pages for David-J-R/BEclear
Correction of batch effects in DNA methylation data
| BEclear-example-methylation-data | Example data set for the BEclear-package |
| BEclear-example-sample-data | Example data set for the BEclear-package |
| BEclear-package | Correction of batch effects in DNA methylation data |
| calcBatchEffects | Calculate the Batch Effects in a given data set |
| calcBatchEffectsForBatch | calcBatchEffectsForBatch |
| calcBlockFrame | calcBlockFrame |
| calcPositions | calcPositions |
| calcScore | calculate batch effect score |
| calcSummary | Summarize median comparison and p-value calculation results |
| clearBEgenes | Prepare a data matrix for the BEclear function |
| combineBlocks | combineBlocks |
| correctBatchEffect | Correct a batch effect in DNA methylation data |
| countValuesToPredict | Count NA entries in a matrix |
| ex.corrected.data | Example matrix of corrected data for the BEclear-package |
| findOutsideValues | Find DNA methylation values out of the boundaries |
| gdepoch | gdepoch |
| imputeMissingData | Matrix prediction using a Latent Factor Model |
| imputeMissingDataForBlock | imputeMissingDataForBlock |
| localLoss | Calculating the Local Loss |
| loss | loss |
| makeBoxplot | produce simple predefined boxplot for methylation data |
| preprocessBEclear | preprocessBEclear |
| replaceOutsideValues | Replace DNA methylation values out of the boundaries |
| runGradientDescent | runGradientDescent |
