NAMESPACE

# Generated by roxygen2: do not edit by hand

export(.readDataTable)
export(ANOVA.Anal)
export(ANOVA2.Anal)
export(AddErrMsg)
export(CalculateFeatureRanking)
export(CalculateGlobalTestScore)
export(CalculateHyperScore)
export(CalculateImpVarCutoff)
export(CalculateOraScore)
export(CalculateQeaScore)
export(CalculateSSP)
export(CentroidCheck)
export(CheckMetaDataConsistency)
export(CleanDataMatrix)
export(ContainMissing)
export(Convert2Mummichog)
export(Convert2MummichogMetaPath)
export(CovariateScatter.Anal)
export(CreateANOVAdoc)
export(CreateAOV2doc)
export(CreateASCAdoc)
export(CreateAnalNullMsg)
export(CreateBiomarkerInputDoc)
export(CreateBiomarkerIntr)
export(CreateBiomarkerOverview)
export(CreateBiomarkerRatioOverview)
export(CreateBiomarkerRnwReport)
export(CreateCorrDoc)
export(CreateEBAMdoc)
export(CreateEnrichAnalDoc)
export(CreateEnrichInputDoc)
export(CreateEnrichIntr)
export(CreateEnrichORAdoc)
export(CreateEnrichOverview)
export(CreateEnrichProcessDoc)
export(CreateEnrichQEAdoc)
export(CreateEnrichRnwReport)
export(CreateEnrichSSPdoc)
export(CreateFooter)
export(CreateGSEAAnalTable)
export(CreateGraph)
export(CreateHCdoc)
export(CreateHeatmap2doc)
export(CreateIntegPathwayAnalysisRnwReport)
export(CreateIntegratedPathwayAnalInputDoc)
export(CreateIntegratedPathwayAnalIntr)
export(CreateIntegratedPathwayDoc)
export(CreateIntegratedPathwayGeneMapTable)
export(CreateIntegratedPathwayNameMapTable)
export(CreateIntegratedPathwayResultsTable)
export(CreateKMdoc)
export(CreateMBdoc)
export(CreateMappingResultTable)
export(CreateMetaAnalTable)
export(CreateMetaAnalysisDEdoc)
export(CreateMetaAnalysisInputDoc)
export(CreateMetaAnalysisIntr)
export(CreateMetaAnalysisNORMdoc)
export(CreateMetaAnalysisOutput)
export(CreateMetaAnalysisOverview)
export(CreateMetaAnalysisRnwReport)
export(CreateMetaMummichogInputDoc)
export(CreateMetaMummichogIntro)
export(CreateMetaMummichogResults)
export(CreateMetaPathRnwReport)
export(CreateMetaTable)
export(CreateModelBiomarkersDoc)
export(CreateMultiBiomarkersDoc)
export(CreateMummichogAnalTable)
export(CreateMummichogAnalysisDoc)
export(CreateMummichogInputDoc)
export(CreateMummichogIntro)
export(CreateMummichogLibs)
export(CreateMummichogMetaAnalPathTable)
export(CreateMummichogMetaAnalReport)
export(CreateMummichogOverview)
export(CreateMummichogRnwReport)
export(CreateNORMdoc)
export(CreateNetworkExplorerDoc)
export(CreateNetworkExplorerInputDoc)
export(CreateNetworkExplorerIntr)
export(CreateNetworkExplorerOverview)
export(CreateNetworkExplorerRnwReport)
export(CreateNetworkGeneMapTable)
export(CreateNetworkNameMapTable)
export(CreateOPLSDAdoc)
export(CreatePCAdoc)
export(CreatePLSdoc)
export(CreatePathAnalDoc)
export(CreatePathInputDoc)
export(CreatePathIntr)
export(CreatePathProcessDoc)
export(CreatePathResultDoc)
export(CreatePathRnwReport)
export(CreatePowerAnalDoc)
export(CreatePowerInputDoc)
export(CreatePowerIntr)
export(CreatePowerOverview)
export(CreatePowerParametersDoc)
export(CreatePowerRnwReport)
export(CreateRFdoc)
export(CreateRHistAppendix)
export(CreateROCLabelsTable)
export(CreateRatioTable)
export(CreateRawAnalysisRnwReport)
export(CreateSAMdoc)
export(CreateSOMdoc)
export(CreateSPLSDAdoc)
export(CreateSVMdoc)
export(CreateStatIOdoc)
export(CreateStatIntr)
export(CreateStatRnwReport)
export(CreateSummaryTable)
export(CreateTimeSeriesAnalNullMsg)
export(CreateTimeSeriesIOdoc)
export(CreateTimeSeriesRnwReport)
export(CreateUNIVdoc)
export(CreateUnivROCTable)
export(CreateUnivarBiomarkersDoc)
export(CreateVennMetaTable)
export(CreateiPCAdoc)
export(CrossReferencing)
export(EBAM.Init)
export(FC.Anal)
export(FeatureCorrelation)
export(FilterVariable)
export(GeneratePeakList)
export(Get.ConcRef)
export(Get.asca.tss)
export(GetAbundanceLabel)
export(GetAccuracyInfo)
export(GetAllDataNames)
export(GetAllKMClusterMembers)
export(GetAllSOMClusterMembers)
export(GetCandidateList)
export(GetCircleInfo)
export(GetCompoundDetails)
export(GetFC)
export(GetFeatureNumbers)
export(GetFinalNameMap)
export(GetFisherPvalue)
export(GetGroupNames)
export(GetHTMLMetSet)
export(GetHTMLPathSet)
export(GetKEGGNodeInfo)
export(GetLassoFreqs)
export(GetLimmaResTable)
export(GetMapTable)
export(GetMetSetName)
export(GetMetaResultMatrix)
export(GetMsetLibCheckMsg)
export(GetMummichogPathSetDetails)
export(GetNMDRStudy)
export(GetNetworkGeneMappingResultTable)
export(GetNewSampleNames)
export(GetORA.pathNames)
export(GetORATable)
export(GetQEA.pathNames)
export(GetQEATable)
export(GetRCommandHistory)
export(GetRFConf.Table)
export(GetROC.coords)
export(GetSSPTable)
export(GetSampleSizeLadder)
export(GetSigTable)
export(GetSigTable.ASCA)
export(GetSigTable.Anova)
export(GetSigTable.Aov2)
export(GetSigTable.Corr)
export(GetSigTable.EBAM)
export(GetSigTable.FC)
export(GetSigTable.MB)
export(GetSigTable.RF)
export(GetSigTable.SAM)
export(GetSigTable.SVM)
export(GetSigTable.TT)
export(GetSigTable.Volcano)
export(GetVariableLabel)
export(GroupPeakList)
export(ImputeMissingVar)
export(InitDataObjects)
export(InitMSObjects)
export(InitPowerAnal)
export(InitStatAnalMode)
export(InitTimeSeriesAnal)
export(InitializaPlan)
export(IsSmallSmplSize)
export(Kmeans.Anal)
export(ListNMDRStudies)
export(Match.Pattern)
export(MergeDuplicates)
export(MetaPathNormalization)
export(MetaboliteMappingExact)
export(Normalization)
export(OPLSDA.Permut)
export(OPLSR.Anal)
export(PCA.Anal)
export(PCA.Flip)
export(PLSDA.CV)
export(PLSDA.Permut)
export(PLSR.Anal)
export(Perform.ASCA)
export(Perform.ASCA.permute)
export(Perform.Permut)
export(Perform.UnivROC)
export(Perform.permutation)
export(PerformAdductMapping)
export(PerformApproxMatch)
export(PerformBatchCorrection)
export(PerformCV.explore)
export(PerformCV.test)
export(PerformCmpdMapping)
export(PerformCurrencyMapping)
export(PerformDataInspect)
export(PerformDataTrimming)
export(PerformDetailMatch)
export(PerformEachDEAnal)
export(PerformGeneMapping)
export(PerformIndNormalization)
export(PerformIntegPathwayAnalysis)
export(PerformKOEnrichAnalysis_KO01100)
export(PerformLimmaDE)
export(PerformMetaMerge)
export(PerformMetaPSEA)
export(PerformMultiMatch)
export(PerformPSEA)
export(PerformParamsOptimization)
export(PerformPeakProfiling)
export(PerformPowerProfiling)
export(PerformPvalCombination)
export(PerformROIExtraction)
export(PerformSignalDriftCorrection)
export(PerformVoteCounting)
export(Plot.Permutation)
export(Plot.sampletrend)
export(PlotANOVA)
export(PlotANOVA2)
export(PlotASCA.Permutation)
export(PlotASCAModel)
export(PlotAccuracy)
export(PlotAscaImpVar)
export(PlotClustPCA)
export(PlotCmpdSummary)
export(PlotCmpdView)
export(PlotConcRange)
export(PlotCorr)
export(PlotCorrHeatMap)
export(PlotDetailROC)
export(PlotEBAM.Cmpd)
export(PlotEnrichDotPlot)
export(PlotEnrichNet.Overview)
export(PlotFC)
export(PlotHCTree)
export(PlotHeatMap)
export(PlotHeatMap2)
export(PlotImpVar)
export(PlotImpVarMeta)
export(PlotImpVars)
export(PlotInmexGraph)
export(PlotInmexPath)
export(PlotIntegPaths)
export(PlotInteraction)
export(PlotKEGGPath)
export(PlotKmeans)
export(PlotMBTimeProfile)
export(PlotMSEA.Overview)
export(PlotMSPeaksPerm)
export(PlotMetpaPath)
export(PlotModelScree)
export(PlotNormSummary)
export(PlotOPLS.Imp)
export(PlotOPLS.MDL)
export(PlotOPLS.Permutation)
export(PlotOPLS.Splot)
export(PlotOPLS2DScore)
export(PlotORA)
export(PlotPCA.overview)
export(PlotPCA2DScore)
export(PlotPCA3DLoading)
export(PlotPCA3DScore)
export(PlotPCA3DScoreImg)
export(PlotPCABiplot)
export(PlotPCALoading)
export(PlotPCAPairSummary)
export(PlotPCAScree)
export(PlotPLS.Classification)
export(PlotPLS.Imp)
export(PlotPLS.Permutation)
export(PlotPLS2DScore)
export(PlotPLS3DLoading)
export(PlotPLS3DScore)
export(PlotPLS3DScoreImg)
export(PlotPLSLoading)
export(PlotPLSPairSummary)
export(PlotPathSummary)
export(PlotPathwayMetaAnalysis)
export(PlotPeaks2Paths)
export(PlotPowerProfile)
export(PlotPowerStat)
export(PlotProbView)
export(PlotQEA.MetSet)
export(PlotQEA.Overview)
export(PlotRF.Classify)
export(PlotRF.ClassifyMeta)
export(PlotRF.Outlier)
export(PlotRF.VIP)
export(PlotRF.VIPMeta)
export(PlotROC)
export(PlotROC.LRmodel)
export(PlotROCTest)
export(PlotRSVM.Classification)
export(PlotRSVM.Cmpd)
export(PlotRocUnivBoxPlot)
export(PlotSAM.Cmpd)
export(PlotSAM.FDR)
export(PlotSOM)
export(PlotSPLS2DScore)
export(PlotSPLS3DLoading)
export(PlotSPLS3DScore)
export(PlotSPLS3DScoreImg)
export(PlotSPLSDA.Classification)
export(PlotSPLSLoading)
export(PlotSPLSPairSummary)
export(PlotSampleNormSummary)
export(PlotSelectedFeature)
export(PlotSubHeatMap)
export(PlotTT)
export(PlotTestAccuracy)
export(PlotVolcano)
export(PlotXIC)
export(Predict.class)
export(PrepareIntegData)
export(PrepareKeggQueryJson)
export(PrepareMetaPath)
export(PrepareNetworkData)
export(PreparePDFReport)
export(PreparePermResult)
export(PreparePrenormData)
export(PrepareQueryJson)
export(PrepareROCData)
export(PrepareROCDetails)
export(PrepareUpsetData)
export(RF.Anal)
export(RF.AnalMeta)
export(ROCPredSamplesTable)
export(RSVM.Anal)
export(Read.BatchDataBC)
export(Read.BatchDataTB)
export(Read.PeakList)
export(Read.PeakListData)
export(Read.SignalDriftData)
export(Read.TextData)
export(Read.TextDataTs)
export(Read.mzTab)
export(ReadIndData)
export(ReadMetaData)
export(ReadMetaPathTable)
export(ReadMetaPathTableMix)
export(ReadPairFile)
export(RecordRCommand)
export(RegisterData)
export(RemoveCmpd)
export(RemoveData)
export(RemoveDuplicates)
export(RemoveGene)
export(RemoveMissingPercent)
export(ReplaceMin)
export(RerenderMetPAGraph)
export(SAM.Anal)
export(SOM.Anal)
export(SPLSR.Anal)
export(SanityCheckData)
export(SanityCheckIndData)
export(SanityCheckMeta)
export(SanityCheckMetaPathTable)
export(SanityCheckMummichogData)
export(SaveTransformedData)
export(SearchByCompound)
export(SearchByName)
export(SearchMsetLibraries)
export(SearchNetDB)
export(SelectMultiData)
export(SetAnalysisMode)
export(SetCachexiaSetUsed)
export(SetCandidate)
export(SetCurrentGroups)
export(SetCurrentMsetLib)
export(SetCustomData)
export(SetDataTypeOfMeta)
export(SetDesignType)
export(SetKEGG.PathLib)
export(SetMetabolomeFilter)
export(SetMummichogPval)
export(SetMummichogPvalFromPercent)
export(SetOrganism)
export(SetPeakEnrichMethod)
export(SetPeakFormat)
export(SetPeakList.GroupValues)
export(SetPeakParam)
export(SetRTincluded)
export(SetSMPDB.PathLib)
export(Setup.AdductData)
export(Setup.BiofluidType)
export(Setup.ConcData)
export(Setup.HMDBReferenceMetabolome)
export(Setup.KEGGReferenceMetabolome)
export(Setup.MapData)
export(Setup.UserMsetLibData)
export(SetupKEGGLinks)
export(SetupSMPDBLinks)
export(SumNorm)
export(Ttests.Anal)
export(UnzipUploadedFile)
export(UpdateData)
export(UpdateEC_Rules)
export(UpdateGraphSettings)
export(UpdateInstrumentParameters)
export(UpdateIntegPathwayAnalysis)
export(UpdateOPLS.Splot)
export(UpdatePCA.Loading)
export(UpdatePLS.Loading)
export(Volcano.Anal)
export(XSet2MSet)
export(doCompoundMapping)
export(doGeneIDMapping)
export(doKEGG2NameMapping)
export(getDataFromTextArea)
export(iPCA.Anal)
export(make_cpdlist)
export(make_ecpdlist)
export(performMB)
export(plotMSfeature)
export(plotProfile)
export(plotSingleTIC)
export(plot_dist)
export(savePeakListMetaData)
export(setInclusionDataSets)
export(splsda)
import(BiocParallel)
import(RColorBrewer)
import(RSQLite)
import(edgeR)
import(fgsea)
import(ggplot2)
import(glasso)
import(gplots)
import(igraph)
import(impute)
import(lattice)
import(methods)
import(qs)
import(scales)
import(siggenes)
importFrom(Cairo,Cairo)
importFrom(MASS,rlm)
importFrom(caret,R2)
importFrom(caret,plsda)
importFrom(caret,train)
importFrom(caret,varImp)
importFrom(crmn,standardsFit)
importFrom(data.table,fread)
importFrom(data.table,setDF)
importFrom(dplyr,enquo)
importFrom(dplyr,group_vars)
importFrom(dplyr,grouped_df)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,tbl_vars)
importFrom(grDevices,colorRampPalette)
importFrom(pROC,plot.roc)
importFrom(pROC,smooth)
importFrom(pcaMethods,pca)
importFrom(plotly,add_markers)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plyr,.)
importFrom(plyr,ddply)
importFrom(plyr,id)
importFrom(plyr,join)
importFrom(plyr,split_labels)
importFrom(plyr,summarise)
importFrom(qs,qread)
importFrom(qs,qsave)
importFrom(rlang,eval_tidy)
importFrom(stats,aggregate)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(vctrs,vec_as_location2)
importFrom(vctrs,vec_as_subscript2)
useDynLib(MetaboAnalystR, .registration=TRUE)