# Generated by roxygen2: do not edit by hand

S3method(arrange,qseaSet)
S3method(filter,qseaSet)
S3method(left_join,mesaDimRed)
S3method(left_join,qseaSet)
S3method(mutate,mesaDimRed)
S3method(mutate,qseaSet)
S3method(pull,qseaSet)
S3method(select,qseaSet)
S3method(sort,qseaSet)
export("%>%")
export(addBamCoveragePairedAndUnpaired)
export(addHMMcopyCNV)
export(addHyperStableFraction)
export(addLibraryInformation)
export(addMedipsEnrichmentFactors)
export(addNormalisation)
export(addSummaryAcrossWindows)
export(annotateWindows)
export(asValidGranges)
export(calculateCGEnrichment)
export(calculateCGEnrichmentGRanges)
export(calculateDMRs)
export(calculateFractionReadsInGRanges)
export(calculateGenomicCGDistribution)
export(combineQsets)
export(combineQsetsList)
export(convertToArrayBetaTable)
export(countWindowsAboveCutoff)
export(downSample)
export(filterByNonOverlaps)
export(filterByOverlaps)
export(filterWindows)
export(fitQseaGLM)
export(getBetaTable)
export(getCountTable)
export(getDMRsData)
export(getDataTable)
export(getDimRed)
export(getGenomicFeatureDistribution)
export(getMart)
export(getMesaAnnoDb)
export(getMesaGenome)
export(getMesaParallel)
export(getMesaTxDb)
export(getNRPMTable)
export(getPCA)
export(getPattern)
export(getSampleQCSummary)
export(getUMAP)
export(getWindowNames)
export(getWindows)
export(is.qseaSet)
export(liftOverHg19)
export(makeAllContrasts)
export(makeQset)
export(makeTransposedTable)
export(mesaDimRed)
export(mesaPCA)
export(mesaUMAP)
export(mixSamples)
export(pivotDMRsLonger)
export(plotCNVheatmap)
export(plotCorrelationMatrix)
export(plotDMRUpset)
export(plotDimRed)
export(plotGeneHeatmap)
export(plotGenomicFeatureDistribution)
export(plotPCA.mesaDimRed)
export(plotRegionsHeatmap)
export(plotUMAP)
export(poolSamples)
export(qseaTableToChrGRanges)
export(removeCNV)
export(removeLibraryFactors)
export(removeNormMethodSuffix)
export(renameQsetNames)
export(renameSamples)
export(runHMMCopy)
export(selectQset)
export(setMart)
export(setMesaAnnoDb)
export(setMesaGenome)
export(setMesaParallel)
export(setMesaTxDb)
export(sliceDMRs)
export(subsetQset)
export(subsetWindowsBySignal)
export(subsetWindowsOverBackground)
export(summariseAcrossWindows)
export(summariseDMRsByContrast)
export(summariseDMRsByGene)
export(writeBigWigs)
export(writeDMRsToBed)
export(writeDMRsToExcel)
exportClasses(mesaDimRed)
exportClasses(mesaPCA)
exportClasses(mesaUMAP)
exportMethods(colnames)
exportMethods(getMart)
exportMethods(setMart)
importFrom(BiocGenerics,colnames)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(glue,glue)
importFrom(magrittr,"%>%")
importFrom(rlang,":=")
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
