Files in uds-helms/BEclear

Correction of batch effects in DNA methylation data

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md R/BEclear.R R/RcppExports.R R/calcBatchEffects.R R/calcBatchEffectsForBatch.R R/calcBlockFrame.R R/calcPositions.R R/calcScore.R R/calcSummary.R R/clearBEgenes.R R/combineBlocks.R R/correctBatchEffect.R R/countValuesToPredict.R R/findOutsideValues.R R/gdepoch.R R/imputeMissingData.R R/imputeMissingDataForBlock.R R/loss.R R/makeBoxplot.R R/preprocessBEclear.R R/replaceOutsideValues.R R/runGradientDescent.R README.md man/BEclear-example-methylation-data.Rd man/BEclear-example-sample-data.Rd man/BEclear-package.Rd man/calcBatchEffects.Rd man/calcBatchEffectsForBatch.Rd man/calcBlockFrame.Rd man/calcPositions.Rd man/calcScore.Rd man/calcSummary.Rd man/clearBEgenes.Rd man/combineBlocks.Rd man/correctBatchEffect.Rd man/countValuesToPredict.Rd man/ex.corrected.data.Rd man/findOutsideValues.Rd man/gdepoch.Rd man/imputeMissingData.Rd man/imputeMissingDataForBlock.Rd man/localLoss.Rd man/loss.Rd man/makeBoxplot.Rd man/preprocessBEclear.Rd man/replaceOutsideValues.Rd man/runGradientDescent.Rd tests/testthat.R tests/testthat/test_calcBatchEffects.R tests/testthat/test_calcBatchEffectsForBatch.R tests/testthat/test_calcBlockFrame.R tests/testthat/test_calcPositions.R tests/testthat/test_calcScore.R tests/testthat/test_calcSummary.R tests/testthat/test_correctBatchEffect.R tests/testthat/test_findOutsideValues.R tests/testthat/test_gdepoch.R tests/testthat/test_imputeMissingData.R tests/testthat/test_localLoss.R tests/testthat/test_loss.R tests/testthat/test_replaceOutsideValues.R tests/testthat/test_runGradientDescent.R vignettes/BEclear.Rmd