# Generated by roxygen2: do not edit by hand

export(C3SDBAdducts)
export(COMStop)
export(GenFormAdducts)
export(MSLibrary)
export(MSPeakLists)
export(MSPeakListsSet)
export(MSPeakListsUnset)
export(MetFragAdducts)
export(TPLogicTransformations)
export(addAllDAEICs)
export(addDAEIC)
export(adduct)
export(annotateSuspects)
export(as.adduct)
export(availableBackends)
export(calculateIonFormula)
export(calculateNeutralFormula)
export(clearCache)
export(components)
export(componentsCamera)
export(componentsCliqueMS)
export(componentsClust)
export(componentsFeatures)
export(componentsIntClust)
export(componentsNT)
export(componentsNTSet)
export(componentsNTUnset)
export(componentsOpenMS)
export(componentsSet)
export(componentsSpecClust)
export(componentsTPs)
export(componentsUnset)
export(compoundScorings)
export(compounds)
export(compoundsCluster)
export(compoundsConsensusSet)
export(compoundsMF)
export(compoundsSIRIUS)
export(compoundsSet)
export(compoundsUnset)
export(convertCCSToMobility)
export(convertMSFiles)
export(convertMSFilesBruker)
export(convertMSFilesIMSCollapse)
export(convertMSFilesOpenMS)
export(convertMSFilesPWiz)
export(convertMSFilesPaths)
export(convertMSFilesTIMSCONVERT)
export(convertMobilityToCCS)
export(createCOMReference)
export(defaultLim)
export(defaultOpenMSAdducts)
export(featureAnnotations)
export(featureGroupQualities)
export(featureGroups)
export(featureGroupsBruker)
export(featureGroupsComparison)
export(featureGroupsComparisonSet)
export(featureGroupsConsensus)
export(featureGroupsEnviMass)
export(featureGroupsGreedy)
export(featureGroupsIMS)
export(featureGroupsKPIC2)
export(featureGroupsOpenMS)
export(featureGroupsSIRIUS)
export(featureGroupsScreening)
export(featureGroupsScreeningSet)
export(featureGroupsSet)
export(featureGroupsSetScreeningUnset)
export(featureGroupsUnset)
export(featureGroupsXCMS)
export(featureGroupsXCMS3)
export(featureQualities)
export(featureQualityNames)
export(features)
export(featuresBruker)
export(featuresConsensus)
export(featuresEnviPick)
export(featuresKPIC2)
export(featuresOpenMS)
export(featuresPiek)
export(featuresSAFD)
export(featuresSIRIUS)
export(featuresSet)
export(featuresUnset)
export(featuresXCMS)
export(featuresXCMS3)
export(findFeatures)
export(findFeaturesBruker)
export(findFeaturesEnviPick)
export(findFeaturesKPIC2)
export(findFeaturesOpenMS)
export(findFeaturesPiek)
export(findFeaturesSAFD)
export(findFeaturesSIRIUS)
export(findFeaturesXCMS)
export(findFeaturesXCMS3)
export(formulaScorings)
export(formulas)
export(formulasConsensusSet)
export(formulasSIRIUS)
export(formulasSet)
export(formulasUnset)
export(genFormulaTPLibrary)
export(genIDLevelRulesFile)
export(genLimitsFile)
export(genReportSettingsFile)
export(generateAnalysisInfo)
export(generateAnalysisInfoFromEnviMass)
export(generateFGroupsOptPSet)
export(generateFeatureOptPSet)
export(generateTPs)
export(generateTPsAnnComp)
export(generateTPsAnnForm)
export(generateTPsBioTransformer)
export(generateTPsCTS)
export(generateTPsLibrary)
export(generateTPsLibraryFormula)
export(getBGMSMSPeaks)
export(getCCSParams)
export(getDACalibrationError)
export(getDefAvgPListParams)
export(getDefEICParams)
export(getDefEIMParams)
export(getDefFGroupsOptParamRanges)
export(getDefFeaturesOptParamRanges)
export(getDefIsolatePrecParams)
export(getDefPeakParams)
export(getDefPredAggrParams)
export(getDefSpecSimParams)
export(getDefTPStructParams)
export(getEICs)
export(getFCParams)
export(getIMSMatchParams)
export(getIMSRangeParams)
export(getLimIMS)
export(getMCTrainData)
export(getMSConversionFormats)
export(getMSConversionTypes)
export(getMSFileFormats)
export(getMSFileTypes)
export(getPiekEICParams)
export(getQuantCalibFromScreening)
export(groupFeaturesSIRIUS)
export(importCheckFeaturesSession)
export(importFeatureGroups)
export(importFeatureGroupsBrukerPA)
export(importFeatureGroupsBrukerTASQ)
export(importFeatureGroupsEnviMass)
export(importFeatureGroupsKPIC2)
export(importFeatureGroupsTable)
export(importFeatureGroupsXCMS)
export(importFeatureGroupsXCMS3)
export(importFeatures)
export(importFeaturesEnviMass)
export(importFeaturesKPIC2)
export(importFeaturesTable)
export(importFeaturesXCMS)
export(importFeaturesXCMS3)
export(installC3SDB)
export(installTIMSCONVERT)
export(loadCacheData)
export(loadMSLibrary)
export(loadMSLibraryMSP)
export(loadMSLibraryMoNAJSON)
export(makeFileHash)
export(makeHash)
export(newProject)
export(numericIDLevel)
export(optimizationResult)
export(optimizeFeatureFinding)
export(optimizeFeatureGrouping)
export(predictCheckFeaturesSession)
export(printPackageOpts)
export(recalibrarateDAFiles)
export(reportHTML)
export(revertDAAnalyses)
export(saveCacheData)
export(setDAMethod)
export(showDataAnalysis)
export(transformationProducts)
export(transformationProductsAnnComp)
export(transformationProductsAnnForm)
export(transformationProductsFormula)
export(transformationProductsLogic)
export(transformationProductsStructure)
export(verifyDependencies)
export(withOpt)
export(workflowStep)
export(workflowStepSet)
exportClasses(MSLibrary)
exportClasses(MSPeakLists)
exportClasses(MSPeakListsSet)
exportClasses(MSPeakListsUnset)
exportClasses(adduct)
exportClasses(components)
exportClasses(componentsCamera)
exportClasses(componentsCliqueMS)
exportClasses(componentsClust)
exportClasses(componentsFeatures)
exportClasses(componentsIntClust)
exportClasses(componentsNT)
exportClasses(componentsNTSet)
exportClasses(componentsNTUnset)
exportClasses(componentsOpenMS)
exportClasses(componentsSet)
exportClasses(componentsSpecClust)
exportClasses(componentsTPs)
exportClasses(componentsUnset)
exportClasses(compounds)
exportClasses(compoundsCluster)
exportClasses(compoundsConsensusSet)
exportClasses(compoundsMF)
exportClasses(compoundsSIRIUS)
exportClasses(compoundsSet)
exportClasses(compoundsUnset)
exportClasses(featureAnnotations)
exportClasses(featureGroups)
exportClasses(featureGroupsBruker)
exportClasses(featureGroupsComparison)
exportClasses(featureGroupsComparisonSet)
exportClasses(featureGroupsConsensus)
exportClasses(featureGroupsEnviMass)
exportClasses(featureGroupsGreedy)
exportClasses(featureGroupsIMS)
exportClasses(featureGroupsKPIC2)
exportClasses(featureGroupsOpenMS)
exportClasses(featureGroupsSIRIUS)
exportClasses(featureGroupsScreening)
exportClasses(featureGroupsScreeningSet)
exportClasses(featureGroupsSet)
exportClasses(featureGroupsSetScreeningUnset)
exportClasses(featureGroupsUnset)
exportClasses(featureGroupsXCMS)
exportClasses(featureGroupsXCMS3)
exportClasses(features)
exportClasses(featuresBruker)
exportClasses(featuresConsensus)
exportClasses(featuresEnviPick)
exportClasses(featuresKPIC2)
exportClasses(featuresOpenMS)
exportClasses(featuresPiek)
exportClasses(featuresSAFD)
exportClasses(featuresSIRIUS)
exportClasses(featuresSet)
exportClasses(featuresUnset)
exportClasses(featuresXCMS)
exportClasses(featuresXCMS3)
exportClasses(formulas)
exportClasses(formulasConsensusSet)
exportClasses(formulasSIRIUS)
exportClasses(formulasSet)
exportClasses(formulasUnset)
exportClasses(optimizationResult)
exportClasses(transformationProducts)
exportClasses(transformationProductsAnnComp)
exportClasses(transformationProductsAnnForm)
exportClasses(transformationProductsFormula)
exportClasses(transformationProductsLogic)
exportClasses(transformationProductsStructure)
exportClasses(workflowStep)
exportClasses(workflowStepSet)
exportMethods("$")
exportMethods("[")
exportMethods("[[")
exportMethods("adducts<-")
exportMethods("analysisInfo<-")
exportMethods(addFormulaScoring)
exportMethods(adducts)
exportMethods(algorithm)
exportMethods(analyses)
exportMethods(analysisInfo)
exportMethods(annotatedPeakList)
exportMethods(annotations)
exportMethods(as.character)
exportMethods(as.data.frame)
exportMethods(as.data.table)
exportMethods(assignMobilities)
exportMethods(averagedPeakLists)
exportMethods(calculateConcs)
exportMethods(calculatePeakQualities)
exportMethods(calculateTox)
exportMethods(checkComponents)
exportMethods(checkFeatures)
exportMethods(clusterProperties)
exportMethods(clusters)
exportMethods(comparison)
exportMethods(componentInfo)
exportMethods(componentTable)
exportMethods(compoundViewer)
exportMethods(concentrations)
exportMethods(consensus)
exportMethods(convertToMFDB)
exportMethods(convertToSuspects)
exportMethods(cutClusters)
exportMethods(defaultExclNormScores)
exportMethods(delete)
exportMethods(estimateIDConfidence)
exportMethods(expandForIMS)
exportMethods(experimentInfo)
exportMethods(export)
exportMethods(featureTable)
exportMethods(filter)
exportMethods(findFGroup)
exportMethods(fromIMS)
exportMethods(generateComponents)
exportMethods(generateComponentsCAMERA)
exportMethods(generateComponentsCliqueMS)
exportMethods(generateComponentsIntClust)
exportMethods(generateComponentsNontarget)
exportMethods(generateComponentsOpenMS)
exportMethods(generateComponentsRAMClustR)
exportMethods(generateComponentsSpecClust)
exportMethods(generateComponentsTPs)
exportMethods(generateCompounds)
exportMethods(generateCompoundsLibrary)
exportMethods(generateCompoundsMetFrag)
exportMethods(generateCompoundsSIRIUS)
exportMethods(generateFormulas)
exportMethods(generateFormulasDA)
exportMethods(generateFormulasGenForm)
exportMethods(generateFormulasSIRIUS)
exportMethods(generateMSPeakLists)
exportMethods(generateMSPeakListsDA)
exportMethods(generateMSPeakListsDAFMF)
exportMethods(generateMSPeakListsMzR)
exportMethods(generateTPsLogic)
exportMethods(getBPCs)
exportMethods(getFeatureQualityNames)
exportMethods(getFeatures)
exportMethods(getMCS)
exportMethods(getPICSet)
exportMethods(getTICs)
exportMethods(getXCMSSet)
exportMethods(getXCMSnExp)
exportMethods(groupFeatIndex)
exportMethods(groupFeatures)
exportMethods(groupFeaturesGreedy)
exportMethods(groupFeaturesKPIC2)
exportMethods(groupFeaturesOpenMS)
exportMethods(groupFeaturesXCMS)
exportMethods(groupFeaturesXCMS3)
exportMethods(groupInfo)
exportMethods(groupNames)
exportMethods(groupQualities)
exportMethods(groupScores)
exportMethods(groupTable)
exportMethods(hasIMS)
exportMethods(identifiers)
exportMethods(internalStandardAssignments)
exportMethods(internalStandards)
exportMethods(launchEICGUI)
exportMethods(length)
exportMethods(lengths)
exportMethods(makeHCluster)
exportMethods(makeSet)
exportMethods(merge)
exportMethods(names)
exportMethods(normInts)
exportMethods(optimizedObject)
exportMethods(optimizedParameters)
exportMethods(overlap)
exportMethods(parents)
exportMethods(peakLists)
exportMethods(plot)
exportMethods(plotBPCs)
exportMethods(plotChord)
exportMethods(plotChroms)
exportMethods(plotChroms3D)
exportMethods(plotGraph)
exportMethods(plotHeatMap)
exportMethods(plotInt)
exportMethods(plotMobilograms)
exportMethods(plotScores)
exportMethods(plotSilhouettes)
exportMethods(plotSpectrum)
exportMethods(plotStructure)
exportMethods(plotTICs)
exportMethods(plotUpSet)
exportMethods(plotVenn)
exportMethods(plotVolcano)
exportMethods(predictRespFactors)
exportMethods(predictTox)
exportMethods(products)
exportMethods(records)
exportMethods(replicateSubtract)
exportMethods(replicates)
exportMethods(report)
exportMethods(reportCSV)
exportMethods(reportPDF)
exportMethods(scores)
exportMethods(screenInfo)
exportMethods(screenSuspects)
exportMethods(selectIons)
exportMethods(setObjects)
exportMethods(sets)
exportMethods(settings)
exportMethods(show)
exportMethods(spectra)
exportMethods(spectrumSimilarity)
exportMethods(spectrumSimilarityIMS)
exportMethods(toxicities)
exportMethods(treeCut)
exportMethods(treeCutDynamic)
exportMethods(unique)
exportMethods(unset)
exportMethods(updateGroups)
import(cluster)
import(data.table)
import(methods)
import(shiny)
importFrom(Rcpp,evalCpp)
importFrom(Rdpack,reprompt)
importFrom(checkmate,makeAssertion)
importFrom(checkmate,vname)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,close.screen)
importFrom(graphics,contour)
importFrom(graphics,grconvertX)
importFrom(graphics,grconvertY)
importFrom(graphics,grid)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,persp)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rasterImage)
importFrom(graphics,rect)
importFrom(graphics,screen)
importFrom(graphics,segments)
importFrom(graphics,split.screen)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(graphics,xinch)
importFrom(graphics,yinch)
importFrom(magrittr,"%>%")
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,heatmap)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,rect.hclust)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,weighted.mean)
importFrom(utils,data)
importFrom(utils,getFromNamespace)
importFrom(utils,head)
importFrom(utils,modifyList)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(withr,defer)
useDynLib(patRoon, .registration = TRUE)
