API for simscr/metaboanalyst
An R Package for Comprehensive Analysis of Metabolomics Data
| Global functions | |
|---|---|
| .compute.mummichog.fgsea | Source code |
| .compute.mummichogSigPvals | Source code |
| .errorF | Source code |
| .get.mSet | Source code |
| .getDdaMS2Scans | Source code |
| .graph.eda | Source code |
| .graph.noa | Source code |
| .graph.sif | Source code |
| .heckbert.nicenum | Source code |
| .perform.mummichogPermutations | Source code |
| .performIntegPathMergeP | Source code |
| .performPathEnrich | Source code |
| .performWeightedZtest | Source code |
| .preparePhenoListSeeds | Source code |
| .read.metaboanalyst.lib | Man page Source code |
| .readDataTable | Man page Source code |
| .search.compoundLib | Source code |
| .set.mSet | Source code |
| .similarityF | Source code |
| ANOVA.Anal | Man page Source code |
| ANOVA2.Anal | Man page Source code |
| ASCAfun.res | Man page Source code |
| ASCAfun1 | Man page |
| ASCAfun2 | Man page |
| AddErrMsg | Man page Source code |
| AddMsg | Source code |
| AutoNorm | Source code |
| CVTest.LRmodel | Man page Source code |
| CalculateCircleInfo | Source code |
| CalculateFeatureRanking | Man page Source code |
| CalculateGlobalTestScore | Man page Source code |
| CalculateHyperScore | Man page Source code |
| CalculateImpVarCutoff | Man page Source code |
| CalculateOraScore | Man page Source code |
| CalculatePairwiseDiff | Man page Source code |
| CalculateQeaScore | Man page Source code |
| CalculateSSP | Man page Source code |
| Check.entry.pls | Source code |
| Check.entry.single | Source code |
| CheckMetaDataConsistency | Man page Source code |
| CleanData | Man page Source code |
| CleanDataMatrix | Man page Source code |
| CleanNames | Source code |
| CleanNumber | Man page Source code |
| ClearNegatives | Man page Source code |
| ClearNumerics | Source code |
| ClearStrings | Man page Source code |
| ClearUserDir | Man page Source code |
| CompNorm | Source code |
| Compound_function_mzlist | Man page Source code |
| ComputeAverageCurve | Man page Source code |
| ComputeColorGradient | Source code |
| ComputeHighLow | Man page Source code |
| ComputeKmeanClusters | Source code |
| ComputeMummichogPermPvals | Source code |
| ComputeSubnetStats | Source code |
| ContainInfiniteTT | Source code |
| ContainInfiniteVolcano | Source code |
| ContainNewSamples | Source code |
| Convert2Mummichog | Man page Source code |
| Covert2Dictionary | Source code |
| CreateANOVAdoc | Man page Source code |
| CreateAOV2doc | Man page Source code |
| CreateASCAdoc | Man page Source code |
| CreateAnalNullMsg | Man page Source code |
| CreateBiomarkerInputDoc | Man page Source code |
| CreateBiomarkerIntr | Man page Source code |
| CreateBiomarkerOverview | Man page Source code |
| CreateBiomarkerRatioOverview | Man page Source code |
| CreateBiomarkerRnwReport | Man page Source code |
| CreateCorrDoc | Man page Source code |
| CreateEBAMdoc | Man page Source code |
| CreateEnrichAnalDoc | Man page Source code |
| CreateEnrichInputDoc | Man page Source code |
| CreateEnrichIntr | Man page Source code |
| CreateEnrichORAdoc | Man page Source code |
| CreateEnrichOverview | Man page Source code |
| CreateEnrichProcessDoc | Man page Source code |
| CreateEnrichQEAdoc | Man page Source code |
| CreateEnrichRnwReport | Man page Source code |
| CreateEnrichSSPdoc | Man page Source code |
| CreateFooter | Man page Source code |
| CreateGSEAAnalTable | Man page Source code |
| CreateGraph | Man page Source code |
| CreateHCdoc | Man page Source code |
| CreateHeader | Source code |
| CreateHeatmap2doc | Man page Source code |
| CreateHeatmapJson | Source code |
| CreateIntegPathwayAnalysisRnwReport | Man page Source code |
| CreateIntegratedPathwayAnalInputDoc | Man page Source code |
| CreateIntegratedPathwayAnalIntr | Man page Source code |
| CreateIntegratedPathwayDoc | Man page Source code |
| CreateIntegratedPathwayGeneMapTable | Man page Source code |
| CreateIntegratedPathwayNameMapTable | Man page Source code |
| CreateIntegratedPathwayResultsTable | Man page Source code |
| CreateKMdoc | Man page Source code |
| CreateLadder | Man page Source code |
| CreateLibFromKEGG | Man page Source code |
| CreateMBdoc | Man page Source code |
| CreateMappingResultTable | Man page Source code |
| CreateMetaAnalTable | Man page Source code |
| CreateMetaAnalysisDEdoc | Man page Source code |
| CreateMetaAnalysisInputDoc | Man page Source code |
| CreateMetaAnalysisIntr | Man page Source code |
| CreateMetaAnalysisNORMdoc | Man page Source code |
| CreateMetaAnalysisOutput | Man page Source code |
| CreateMetaAnalysisOverview | Man page Source code |
| CreateMetaAnalysisRnwReport | Man page Source code |
| CreateMetaTable | Man page Source code |
| CreateModelBiomarkersDoc | Man page Source code |
| CreateMultiBiomarkersDoc | Man page Source code |
| CreateMummichogAnalTable | Man page Source code |
| CreateMummichogAnalysisDoc | Man page Source code |
| CreateMummichogInputDoc | Man page Source code |
| CreateMummichogIntro | Man page Source code |
| CreateMummichogLibs | Man page Source code |
| CreateMummichogOverview | Man page Source code |
| CreateMummichogRnwReport | Man page Source code |
| CreateNORMdoc | Man page Source code |
| CreateNetworkExplorerDoc | Man page Source code |
| CreateNetworkExplorerInputDoc | Man page Source code |
| CreateNetworkExplorerIntr | Man page Source code |
| CreateNetworkExplorerOverview | Man page Source code |
| CreateNetworkExplorerRnwReport | Man page Source code |
| CreateNetworkGeneMapTable | Man page Source code |
| CreateNetworkNameMapTable | Man page Source code |
| CreateOPLSDAdoc | Man page Source code |
| CreatePCAdoc | Man page Source code |
| CreatePLSdoc | Man page Source code |
| CreatePathAnalDoc | Man page Source code |
| CreatePathInputDoc | Man page Source code |
| CreatePathIntr | Man page Source code |
| CreatePathProcessDoc | Man page Source code |
| CreatePathResultDoc | Man page Source code |
| CreatePathRnwReport | Man page Source code |
| CreatePowerAnalDoc | Man page Source code |
| CreatePowerInputDoc | Man page Source code |
| CreatePowerIntr | Man page Source code |
| CreatePowerOverview | Man page Source code |
| CreatePowerParametersDoc | Man page Source code |
| CreatePowerRnwReport | Man page Source code |
| CreateRFdoc | Man page Source code |
| CreateRHistAppendix | Man page Source code |
| CreateROCLabelsTable | Man page Source code |
| CreateRatioTable | Man page Source code |
| CreateSAMdoc | Man page Source code |
| CreateSOMdoc | Man page Source code |
| CreateSPLSDAdoc | Man page Source code |
| CreateSVMdoc | Man page Source code |
| CreateSemiTransColors | Man page Source code |
| CreateStatIOdoc | Man page Source code |
| CreateStatIntr | Man page Source code |
| CreateStatRnwReport | Man page Source code |
| CreateSummaryTable | Man page Source code |
| CreateTimeSeriesAnalNullMsg | Man page Source code |
| CreateTimeSeriesIOdoc | Man page Source code |
| CreateTimeSeriesRnwReport | Man page Source code |
| CreateUNIVdoc | Man page Source code |
| CreateUnivROCTable | Man page Source code |
| CreateUnivarBiomarkersDoc | Man page Source code |
| CreateVennMetaTable | Man page Source code |
| CreateiPCAdoc | Man page Source code |
| CrossReferencing | Man page Source code |
| DecomposeGraph | Source code |
| EBAM.Init | Man page Source code |
| ExcludeNodes | Source code |
| ExportNetwork | Source code |
| ExtractMS2data | Man page Source code |
| ExtractModule | Source code |
| FC.Anal.paired | Man page Source code |
| FC.Anal.unpaired | Man page Source code |
| FeatureCorrelation | Man page Source code |
| FilterVariable | Man page Source code |
| FindCommunities | Source code |
| FisherLSD | Man page Source code |
| FormatPeakList | Man page Source code |
| GeneratePathwayJSON | Source code |
| GenerateTemplates | Source code |
| Get.Accuracy | Source code |
| Get.ConcRef | Man page Source code |
| Get.Fisher | Source code |
| Get.Fstat | Source code |
| Get.Leverage | Man page Source code |
| Get.VIP | Man page Source code |
| Get.asca.leverage | Source code |
| Get.asca.tss | Man page Source code |
| Get.bwss | Man page Source code |
| Get.pAUC | Man page Source code |
| Get.pred | Man page Source code |
| Get.rpart.summary | Man page Source code |
| GetAbundanceLabel | Man page Source code |
| GetAccuracyInfo | Man page Source code |
| GetAdductMsg | Source code |
| GetAllBatchNames | Source code |
| GetAllDataNames | Man page Source code |
| GetAllKMClusterMembers | Man page Source code |
| GetAllSOMClusterMembers | Man page Source code |
| GetAnova2Cmpds | Source code |
| GetAnova2DnMat | Source code |
| GetAnova2LnMat | Source code |
| GetAnova2UpMat | Source code |
| GetAnovaCmpdInxs | Source code |
| GetAnovaCmpds | Source code |
| GetAnovaDnMat | Source code |
| GetAnovaSigFileName | Source code |
| GetAnovaUpMat | Source code |
| GetAov2SigColNames | Source code |
| GetAov2SigFileName | Source code |
| GetAov2SigMat | Source code |
| GetAov2SigRowNames | Source code |
| GetAovPostHocSig | Source code |
| GetAovSigColNames | Source code |
| GetAovSigMat | Source code |
| GetAovSigNum | Source code |
| GetAovSigRowNames | Source code |
| GetAscaSigColNames | Source code |
| GetAscaSigFileName | Source code |
| GetAscaSigMat | Source code |
| GetAscaSigRowNames | Source code |
| GetBashFullPath | Source code |
| GetBestModelIndex | Source code |
| GetCIs | Man page Source code |
| GetCMD | Man page Source code |
| GetCanListRowNumber | Source code |
| GetCandidateList | Man page Source code |
| GetCircleInfo | Man page Source code |
| GetClassLabel | Source code |
| GetColorGradient | Source code |
| GetColorSchema | Source code |
| GetCompoundDetails | Man page Source code |
| GetConvertFullPath | Man page Source code |
| GetCorSigColNames | Source code |
| GetCorSigMat | Source code |
| GetCorSigRowNames | Source code |
| GetCorrSigFileName | Source code |
| GetCurrencyMsg | Source code |
| GetCurrentConfMat | Source code |
| GetCurrentConfMatTest | Source code |
| GetCurrentImg | Source code |
| GetCurrentMsg | Source code |
| GetDataDims | Source code |
| GetDefaultPLSCVComp | Source code |
| GetDefaultPLSPairComp | Source code |
| GetDefaultPvalCutoff | Source code |
| GetDefaultSPLSCVComp | Source code |
| GetDefaultSPLSPairComp | Source code |
| GetEBAMSigColNames | Source code |
| GetEBAMSigMat | Source code |
| GetEBAMSigRowNames | Source code |
| GetEBAMSuggestedA0 | Source code |
| GetErrMsg | Source code |
| GetExtendRange | Man page Source code |
| GetFC | Man page Source code |
| GetFCSigColNames | Source code |
| GetFCSigMat | Source code |
| GetFCSigRowNames | Source code |
| GetFeatureNumbers | Man page Source code |
| GetFeatureRankingMat | Source code |
| GetFinalNameMap | Man page Source code |
| GetFisherPvalue | Man page Source code |
| GetGeneHitsRowNumber | Source code |
| GetGeneMappingResultTable | Source code |
| GetGroupNames | Source code |
| GetGroupNumber | Source code |
| GetHTMLMetSet | Man page Source code |
| GetHTMLPathSet | Man page Source code |
| GetHitsRowNumber | Source code |
| GetImpColNames | Source code |
| GetImpFeatureMat | Man page Source code |
| GetImpHighLow | Source code |
| GetImpRowNames | Source code |
| GetImpValues | Source code |
| GetIntegHTMLPathSet | Source code |
| GetIntegResultColNames | Source code |
| GetIntegResultMatrix | Source code |
| GetIntegResultPathIDs | Source code |
| GetIntegResultPathNames | Source code |
| GetKEGG.PathNames | Source code |
| GetKEGGNodeInfo | Man page Source code |
| GetKMClusterMembers | Man page Source code |
| GetLRConvergence | Source code |
| GetLREquation | Source code |
| GetLR_clsLbl | Source code |
| GetLR_clsLblNew | Source code |
| GetLRmodelTable | Source code |
| GetLRperformTable | Source code |
| GetLRthreshold | Source code |
| GetLassoFreqNames | Source code |
| GetLassoFreqs | Man page Source code |
| GetLimmaResTable | Man page Source code |
| GetLiteralGroupNames | Source code |
| GetMBSigColNames | Source code |
| GetMBSigMat | Source code |
| GetMBSigRowNames | Source code |
| GetMapTable | Man page Source code |
| GetMatchedCompounds | Source code |
| GetMatchingDetails | Source code |
| GetMaxAnova2Inx | Source code |
| GetMaxPCAComp | Man page Source code |
| GetMaxPLSCVComp | Source code |
| GetMaxPLSPairComp | Source code |
| GetMeanROC | Man page Source code |
| GetMetPANodeInfo | Source code |
| GetMetSetName | Man page Source code |
| GetMetaCheckMsg | Source code |
| GetMetaGeneIDType | Source code |
| GetMetaGroupNames | Source code |
| GetMetaResultColNames | Source code |
| GetMetaResultGeneIDLinks | Source code |
| GetMetaResultGeneIDs | Source code |
| GetMetaResultGeneSymbols | Source code |
| GetMetaResultMatrix | Man page Source code |
| GetMetaSanityCheckMsg | Source code |
| GetMetaSigHitsTable | Man page Source code |
| GetMetaStat | Source code |
| GetMetaStatNames | Source code |
| GetMinGroupSize | Source code |
| GetModelNames | Source code |
| GetMsetLibCheckMsg | Man page Source code |
| GetMsetLibSearchResult | Man page Source code |
| GetMsetMembers | Source code |
| GetMsetNames | Man page Source code |
| GetMsetReferences | Source code |
| GetMummiDataType | Source code |
| GetMummiMode | Source code |
| GetMummiResColNames | Source code |
| GetMummiResMatrix | Source code |
| GetMummiResRowNames | Source code |
| GetMummichogHTMLPathSet | Source code |
| GetMummichogMZHits | Source code |
| GetMummichogPathSetDetails | Man page Source code |
| GetNetsEdgeNum | Source code |
| GetNetsName | Source code |
| GetNetsNameString | Source code |
| GetNetsNodeNum | Source code |
| GetNetsQueryNum | Source code |
| GetNetworkGeneMappingResultTable | Man page Source code |
| GetNewSampleGrps | Source code |
| GetNewSampleNameVec | Source code |
| GetNewSampleNames | Man page Source code |
| GetNewSampleProbs | Source code |
| GetNodeBetweenness | Source code |
| GetNodeDegrees | Source code |
| GetNodeEmblEntrezIDs | Source code |
| GetNodeEntrezIDs | Source code |
| GetNodeIDs | Source code |
| GetNodeNames | Source code |
| GetNormGroupNames | Source code |
| GetOPLSLoadAxesSpec | Source code |
| GetOPLSLoadCmpdInxs | Source code |
| GetOPLSLoadCmpds | Source code |
| GetOPLSLoadColNames | Source code |
| GetOPLSLoadMat | Source code |
| GetORA.colorBar | Source code |
| GetORA.keggIDs | Source code |
| GetORA.mat | Source code |
| GetORA.pathNames | Man page Source code |
| GetORA.rowNames | Source code |
| GetORA.smpdbIDs | Man page Source code |
| GetORATable | Man page Source code |
| GetPCALoadAxesSpec | Source code |
| GetPCALoadCmpdInxs | Source code |
| GetPCALoadCmpds | Source code |
| GetPCALoadMat | Source code |
| GetPLSBestTune | Source code |
| GetPLSLoadAxesSpec | Source code |
| GetPLSLoadCmpdInxs | Source code |
| GetPLSLoadCmpds | Source code |
| GetPLSLoadMat | Source code |
| GetPLSSigColNames | Source code |
| GetPLSSigMat | Source code |
| GetPLSSigRowNames | Source code |
| GetPLS_CVColNames | Source code |
| GetPLS_CVMat | Source code |
| GetPLS_CVRowNames | Source code |
| GetPathNames | Source code |
| GetPowerValuesX | Source code |
| GetPrenormClsNms | Source code |
| GetPrenormFeatureNms | Source code |
| GetPrenormFeatureNum | Source code |
| GetPrenormSmplNms | Source code |
| GetQEA.colorBar | Source code |
| GetQEA.keggIDs | Man page Source code |
| GetQEA.mat | Source code |
| GetQEA.pathNames | Man page Source code |
| GetQEA.rowNames | Source code |
| GetQEA.smpdbIDs | Source code |
| GetQEATable | Man page Source code |
| GetQuery | Source code |
| GetRCommandHistory | Man page Source code |
| GetRFConf.Table | Man page Source code |
| GetRFConfColNames | Source code |
| GetRFConfMat | Man page Source code |
| GetRFConfRowNames | Source code |
| GetRFOOB | Man page Source code |
| GetRFSigColNames | Source code |
| GetRFSigMat | Man page Source code |
| GetRFSigRowNames | Source code |
| GetROC.coords | Man page Source code |
| GetROCLassoFreq | Man page Source code |
| GetROCTtestP | Man page Source code |
| GetRandomNumbers | Source code |
| GetRandomSubsetIndex | Source code |
| GetRefLibCheckMsg | Source code |
| GetSAMDeltaRange | Source code |
| GetSAMSigColNames | Source code |
| GetSAMSigMat | Source code |
| GetSAMSigRowNames | Source code |
| GetSMPDBimg | Source code |
| GetSOMClusterMembers | Man page Source code |
| GetSPLSLoadAxesSpec | Source code |
| GetSPLSLoadCmpdInxs | Source code |
| GetSPLSLoadCmpds | Source code |
| GetSPLSLoadMat | Source code |
| GetSPLSSigColNames | Source code |
| GetSPLS_CVColNames | Source code |
| GetSPLS_CVMat | Source code |
| GetSPLS_CVRowNames | Source code |
| GetSSP.Concs | Source code |
| GetSSP.Details | Source code |
| GetSSP.HMDB | Source code |
| GetSSP.Names | Source code |
| GetSSP.Notes | Source code |
| GetSSP.Pmids | Source code |
| GetSSP.RefConc | Source code |
| GetSSP.RefConcs | Source code |
| GetSSP.Refs | Source code |
| GetSSP.States | Source code |
| GetSSPTable | Man page Source code |
| GetSVMSigColNames | Source code |
| GetSVMSigMat | Man page Source code |
| GetSVMSigRowNames | Source code |
| GetSampleSizeLadder | Man page Source code |
| GetSelectedDataNames | Man page Source code |
| GetSelectedDataNumber | Man page Source code |
| GetShapeSchema | Source code |
| GetShortNames | Source code |
| GetShortestPaths | Source code |
| GetSigTable | Man page Source code |
| GetSigTable.ASCA | Man page Source code |
| GetSigTable.Anova | Man page Source code |
| GetSigTable.Aov2 | Man page Source code |
| GetSigTable.Corr | Man page Source code |
| GetSigTable.EBAM | Man page Source code |
| GetSigTable.FC | Man page Source code |
| GetSigTable.MB | Man page Source code |
| GetSigTable.RF | Man page Source code |
| GetSigTable.SAM | Man page Source code |
| GetSigTable.SVM | Man page Source code |
| GetSigTable.TT | Man page Source code |
| GetSigTable.Volcano | Man page Source code |
| GetSuggestedSAMDelta | Man page Source code |
| GetTTSigColNames | Source code |
| GetTTSigMat | Man page Source code |
| GetTTSigRowNames | Source code |
| GetTopInx | Man page Source code Source code |
| GetTrainTestSplitMat | Man page Source code |
| GetTtCmpdInxs | Source code |
| GetTtCmpds | Source code |
| GetTtDnMat | Source code |
| GetTtUpMat | Source code |
| GetTtestRes | Man page Source code |
| GetTtestSigFileName | Source code |
| GetUnivRankedFeatureNames | Source code |
| GetUnivReport | Man page Source code |
| GetVariableLabel | Man page Source code |
| GetVennGeneNames | Man page Source code |
| GetVolcanoCmpdInxs | Source code |
| GetVolcanoCmpds | Source code |
| GetVolcanoDnMat | Source code |
| GetVolcanoHlMat | Source code |
| GetVolcanoRangeX | Source code |
| GetVolcanoSigColNames | Source code |
| GetVolcanoSigMat | Source code |
| GetVolcanoSigRowNames | Source code |
| GetVolcanoUpMat | Source code |
| GetVolcanoVlMat | Source code |
| GetVolcanoVrMat | Source code |
| GetXYCluster | Man page Source code |
| GroupPeakList | Man page Source code |
| HMDBID2KEGGID | Man page Source code |
| HMDBID2Name | Man page Source code |
| ImportRawMSData | Man page Source code |
| ImportRawMSDataList | Man page Source code |
| ImputeVar | Man page Source code |
| InitDataObjects | Man page Source code |
| InitPowerAnal | Man page Source code |
| InitStatAnalMode | Man page Source code |
| InitTimeSeriesAnal | Man page Source code |
| IsDataContainsNegative | Source code |
| IsSmallSmplSize | Man page Source code |
| IsSpectraProcessingOK | Man page Source code |
| KEGGID2HMDBID | Man page Source code |
| KEGGID2Name | Man page Source code |
| KEGGPATHID2SMPDBIDs | Man page Source code |
| Kmeans.Anal | Man page Source code |
| LSD.test | Man page Source code |
| LoadGOLib | Source code |
| LoadKEGGKO_lib | Man page Source code |
| LoadKEGGLib | Man page Source code |
| LoadKEGGLib.gene | Source code |
| LoadKEGGLib_2018 | Source code |
| LoadMotifLib | Source code |
| LoadREACTOMELib.gene | Source code |
| LoadSmpLib | Man page Source code |
| LogNorm | Man page Source code |
| MCVfold.splsda | Source code |
| MSspec.fillPeaks | Man page Source code |
| MSspec.rtCorrection | Man page Source code |
| MapCmpd2KEGGNodes | Man page Source code |
| MapKO2KEGGEdges | Man page Source code |
| Match.Pattern | Man page Source code |
| MeanCenter | Source code |
| MedianNorm | Source code |
| MergeDatasets | Man page Source code |
| MergeDuplicates | Man page Source code |
| MetaboliteMappingExact | Man page Source code |
| Normalization | Man page Source code |
| OPLSDA.Permut | Man page Source code |
| OPLSR.Anal | Man page Source code |
| PCA.Anal | Man page Source code |
| PCA.Flip | Man page Source code |
| PCA.GENES | Man page Source code |
| PLSDA.CV | Man page Source code |
| PLSDA.Permut | Man page Source code |
| PLSR.Anal | Man page Source code |
| ParetoNorm | Source code |
| Perform.ASCA | Man page Source code |
| Perform.ASCA.permute | Man page Source code |
| Perform.Permut | Man page Source code |
| Perform.UnivROC | Man page Source code |
| Perform.permutation | Man page Source code |
| PerformAdductMapping | Man page Source code |
| PerformApproxMatch | Man page Source code |
| PerformBatchCorrection | Man page Source code |
| PerformCV.explore | Man page Source code |
| PerformCV.test | Man page Source code |
| PerformCurrencyMapping | Man page Source code |
| PerformDataNormalization | Source code |
| PerformDetailMatch | Man page Source code |
| PerformEachDEAnal | Man page Source code |
| PerformEnrichAnalysis | Source code |
| PerformFastUnivTests | Source code |
| PerformIndNormalization | Man page Source code |
| PerformIntegCmpdMapping | Man page Source code |
| PerformIntegGeneMapping | Man page Source code |
| PerformIntegPathwayAnalysis | Man page Source code |
| PerformKOEnrichAnalysis_KO01100 | Man page Source code |
| PerformKOEnrichAnalysis_List | Man page Source code |
| PerformLayOut | Source code |
| PerformLimma | Source code |
| PerformLimmaDE | Man page Source code |
| PerformMapping | Man page Source code |
| PerformMetaMerge | Man page Source code |
| PerformMultiMatch | Man page Source code |
| PerformNetEnrichment | Source code |
| PerformPSEA | Man page Source code |
| PerformPeakAnnotation | Man page Source code |
| PerformPeakProfiling | Man page Source code |
| PerformPowerProfiling | Man page Source code |
| PerformPvalCombination | Man page Source code |
| PerformVoteCounting | Man page Source code |
| Plot.Permutation | Man page Source code |
| Plot3D | Source code |
| PlotANOVA | Man page Source code |
| PlotANOVA2 | Man page Source code |
| PlotASCA.Permutation | Man page Source code |
| PlotASCAModel | Man page Source code |
| PlotAccuracy | Man page Source code |
| PlotAscaImpVar | Man page Source code |
| PlotBoxPlot | Man page Source code |
| PlotCmpdSummary | Man page Source code |
| PlotCmpdView | Man page Source code |
| PlotConcRange | Man page Source code |
| PlotConfusion | Source code |
| PlotCorr | Man page Source code |
| PlotCorrHeatMap | Man page Source code |
| PlotDataProfile | Source code |
| PlotDetailROC | Man page Source code |
| PlotEBAM.Cmpd | Man page Source code |
| PlotEIC | Man page Source code |
| PlotEnrichNet.Overview | Man page Source code |
| PlotFC | Man page Source code |
| PlotHCTree | Man page Source code |
| PlotHeatMap | Man page Source code |
| PlotHeatMap2 | Man page Source code |
| PlotImpVar | Man page Source code |
| PlotImpVars | Man page Source code |
| PlotInmexGraph | Man page Source code |
| PlotInmexPath | Man page Source code |
| PlotIntegPaths | Man page Source code |
| PlotInteraction | Man page Source code |
| PlotKEGGPath | Man page Source code |
| PlotKmeans | Man page Source code |
| PlotLoadBoxplot | Source code |
| PlotLoadingCmpd | Man page Source code |
| PlotMBTimeProfile | Man page Source code |
| PlotMS.RT | Man page Source code |
| PlotMS2Spectra | Man page Source code |
| PlotMSEA.Overview | Man page Source code |
| PlotMSPeaksPerm | Man page Source code |
| PlotMetaVenn | Man page Source code |
| PlotMetpaPath | Man page Source code |
| PlotModelScree | Man page Source code |
| PlotNetwork | Source code |
| PlotNormSummary | Man page Source code |
| PlotOPLS.MDL | Man page Source code |
| PlotOPLS.Permutation | Man page Source code |
| PlotOPLS.Splot | Man page Source code |
| PlotOPLS2DScore | Man page Source code |
| PlotORA | Man page Source code |
| PlotPCA.overview | Man page Source code |
| PlotPCA2DScore | Man page Source code |
| PlotPCA3DLoading | Source code |
| PlotPCA3DScore | Man page Source code |
| PlotPCA3DScoreImg | Man page Source code |
| PlotPCABiplot | Man page Source code |
| PlotPCALoading | Man page Source code |
| PlotPCAPairSummary | Man page Source code |
| PlotPCAScree | Man page Source code |
| PlotPLS.Classification | Man page Source code |
| PlotPLS.Imp | Man page Source code |
| PlotPLS.Permutation | Man page Source code |
| PlotPLS2DScore | Man page Source code |
| PlotPLS3DLoading | Source code |
| PlotPLS3DScore | Man page Source code |
| PlotPLS3DScoreImg | Man page Source code |
| PlotPLSLoading | Man page Source code |
| PlotPLSPairSummary | Man page Source code |
| PlotPathSummary | Man page Source code |
| PlotPathwayMZHits | Man page Source code |
| PlotPeaks2Paths | Man page Source code |
| PlotPowerProfile | Man page Source code |
| PlotPowerStat | Man page Source code |
| PlotProbView | Man page Source code |
| PlotQEA.MetSet | Man page Source code |
| PlotQEA.Overview | Man page Source code |
| PlotRF.Classify | Man page Source code |
| PlotRF.Outlier | Man page Source code |
| PlotRF.VIP | Man page Source code |
| PlotROC | Man page Source code |
| PlotROC.LRmodel | Man page Source code |
| PlotROCTest | Man page Source code |
| PlotRSVM.Classification | Man page Source code |
| PlotRSVM.Cmpd | Man page Source code |
| PlotSAM.Cmpd | Man page Source code |
| PlotSAM.FDR | Man page Source code |
| PlotSOM | Man page Source code |
| PlotSPLS2DScore | Man page Source code |
| PlotSPLS3DLoading | Source code |
| PlotSPLS3DScore | Man page Source code |
| PlotSPLS3DScoreImg | Man page Source code Source code |
| PlotSPLSDA.Classification | Man page Source code |
| PlotSPLSLoading | Man page Source code |
| PlotSPLSPairSummary | Man page Source code |
| PlotSampleNormSummary | Man page Source code |
| PlotSelectedFeature | Man page Source code |
| PlotSigVar | Man page Source code |
| PlotSubHeatMap | Man page Source code |
| PlotTT | Man page Source code |
| PlotTestAccuracy | Man page Source code |
| PlotVerticalCmpdSummary | Source code |
| PlotVolcano | Man page Source code |
| Predict.class | Man page Source code |
| Prepare2Venn | Source code |
| Prepare3Venn | Source code |
| Prepare4Venn | Source code |
| PrepareGeneList | Source code |
| PrepareIntegData | Man page Source code |
| PrepareLatex | Source code |
| PrepareNetwork | Source code |
| PrepareNetworkData | Man page Source code |
| PreparePDFReport | Man page Source code |
| PreparePermResult | Man page Source code |
| PreparePrenormData | Man page Source code |
| PrepareQueryJson | Man page Source code |
| PrepareROCData | Man page Source code |
| PrepareROCDetails | Man page Source code |
| PrepareSifDownloads | Source code |
| PrepareSignatureOfMetaboAnalyst | Source code |
| PrepareSubnetDownloads | Source code |
| PrepareVennData | Man page Source code |
| ProbNorm | Source code |
| QuantileNormalize | Source code |
| QueryPhenoSQLite | Source code |
| RF.Anal | Man page Source code |
| ROCPredSamplesTable | Man page Source code |
| RSVM | Man page Source code |
| RSVM.Anal | Man page Source code |
| RangeNorm | Source code |
| RankFeatures | Man page Source code |
| Read.BatchCSVdata | Man page Source code |
| Read.MSspec | Man page Source code |
| Read.PeakList | Man page Source code |
| Read.PeakListData | Man page Source code |
| Read.TextData | Man page Source code |
| ReadIndData | Man page Source code |
| ReadPairFile | Man page Source code |
| RecordRCommand | Man page Source code |
| RegisterData | Man page Source code |
| RemoveCmpd | Man page Source code |
| RemoveData | Man page Source code |
| RemoveDuplicates | Man page Source code |
| RemoveDuplicatesNetwork | Source code |
| RemoveFile | Man page Source code |
| RemoveFolder | Man page Source code |
| RemoveGene | Man page Source code |
| RemoveMissingPercent | Man page Source code |
| ReplaceMin | Man page Source code |
| RequireFastUnivTests | Source code |
| RerenderMetPAGraph | Man page Source code |
| ResetBatchData | Source code |
| SAM.Anal | Man page Source code |
| SOM.Anal | Man page Source code |
| SPLSR.Anal | Man page Source code |
| SanityCheckData | Man page Source code |
| SanityCheckIndData | Man page Source code |
| SanityCheckMummichogData | Man page Source code |
| Save2KEGGJSON | Source code |
| SaveCurrentSession | Source code |
| SaveTransformedData | Man page Source code |
| SearchByCompound | Man page Source code |
| SearchByName | Man page Source code |
| SearchMsetLibraries | Man page Source code |
| SearchNetDB | Man page Source code |
| SelectMultiData | Man page Source code |
| SetAnalysisMode | Man page Source code |
| SetAnnotationParam | Man page Source code |
| SetCachexiaSetUsed | Man page Source code |
| SetCandidate | Man page Source code |
| SetClass | Man page Source code |
| SetCurrentGroups | Man page Source code |
| SetCurrentMsetLib | Man page Source code |
| SetCustomData | Man page Source code |
| SetDesignType | Man page Source code |
| SetKEGG.PathLib | Man page Source code |
| SetMetabolomeFilter | Man page Source code |
| SetMummichogPval | Man page Source code |
| SetMummichogPvalFromPercent | Man page Source code |
| SetOrganism | Man page Source code |
| SetPeakEnrichMethod | Man page Source code |
| SetPeakFormat | Man page Source code |
| SetPeakList.GroupValues | Man page Source code |
| SetPeakParam | Man page Source code |
| SetSMPDB.PathLib | Man page Source code |
| Setup.AdductData | Man page Source code |
| Setup.BiofluidType | Man page Source code |
| Setup.ConcData | Man page Source code |
| Setup.HMDBReferenceMetabolome | Man page Source code |
| Setup.KEGGReferenceMetabolome | Man page Source code |
| Setup.MapData | Man page Source code |
| Setup.UserMsetLibData | Man page Source code |
| SetupKEGGLinks | Man page Source code |
| SetupMSdataMatrix | Man page Source code |
| SetupMetaStats | Source code |
| SetupSMPDBLinks | Man page Source code |
| ShowMemoryUse | Source code |
| SumNorm | Man page Source code |
| Ttests.Anal | Man page Source code |
| UnzipUploadedFile | Man page Source code |
| UpdateData | Man page Source code |
| UpdateGraphSettings | Man page Source code |
| UpdateInstrumentParameters | Man page Source code |
| UpdateIntegPathwayAnalysis | Man page Source code |
| UpdateKmeans | Source code |
| UpdateNetworkLayout | Source code |
| UpdateOPLS.Splot | Man page Source code |
| UpdatePCA.Loading | Man page Source code |
| UpdatePLS.Loading | Man page Source code |
| UpdateSubnetStats | Source code |
| ValidateFeatureName | Source code |
| Volcano.Anal | Man page Source code |
| XSet2MSet | Man page Source code |
| analyze.lipids | Man page Source code |
| aof | Man page Source code |
| aov.between | Man page Source code |
| aov.between.type3 | Source code |
| aov.repeated | Man page Source code |
| aov.within | Man page Source code |
| aov.within.wo | Source code |
| calcGseaStat2 | Source code |
| calculateConcISO | Man page Source code |
| calculateConcNoISO | Source code |
| cleanMem | Source code |
| color_scale | Source code |
| combinePvals | Source code |
| community.significance.test | Source code |
| computeConc | Man page Source code |
| concplot | Source code |
| convert2JsonList | Source code |
| convertIgraph2JSON | Source code |
| count_cpd2mz | Source code |
| createCVset | Man page Source code |
| defl.select | Source code |
| deflation | Source code |
| descendMin | Man page Source code |
| doCompoundMapping | Man page Source code |
| doEntrez2SymbolMapping | Source code |
| doGene2KONameMapping | Source code |
| doGeneIDMapping | Man page Source code |
| doHeatmapMummichogTest | Source code |
| doID2LabelMapping | Source code |
| doKEGG2NameMapping | Man page Source code |
| doKOFiltering | Man page Source code |
| end.with | Source code |
| explained_variance | Source code |
| fgsea2 | Man page Source code |
| fig2dev | Source code |
| fillpathways | Man page Source code |
| findEqualGreaterM | Man page Source code |
| fitFDist | Source code |
| genLREquation | Source code |
| genLogisticRegMdl | Man page Source code |
| generate_breaks | Source code |
| get.BER | Source code |
| get.confusion_matrix | Source code |
| get.name.and.value | Source code |
| getBestHit | Source code |
| getDataFromTextArea | Man page Source code |
| getEdgeLabel | Source code |
| getEdgeLty | Source code |
| getFactorSize | Source code |
| getIdx | Source code |
| getLayout | Source code |
| getVennCounts | Source code |
| getndp | Source code |
| heckbert | Man page Source code |
| hex2rgba | Source code |
| iPCA.Anal | Man page Source code |
| image.plot | Source code |
| image.plot.plt | Source code |
| internal_predict.DA | Source code |
| internal_wrapper.mint | Source code |
| isEmptyMatrix | Man page Source code |
| kwtest | Man page Source code |
| l2.norm | Source code |
| load_RSclient | Source code |
| load_Rserve | Source code |
| load_camera | Source code |
| load_caret | Source code |
| load_data.table | Source code |
| load_ggplot | Source code |
| load_gplots | Source code |
| load_grid | Source code |
| load_igraph | Source code |
| load_kegggraph | Source code |
| load_lattice | Source code |
| load_pls | Source code |
| load_rcolorbrewer | Source code |
| load_reshape | Source code |
| load_rgraphwiz | Source code |
| load_rsqlite | Source code |
| load_stringr | Source code |
| load_xcms | Source code |
| logisticReg | Source code |
| make_cpdlib | Man page Source code |
| make_cpdlist | Man page Source code |
| map | Man page |
| matrix.cov | Source code |
| mb.1D | Source code |
| mb.2D | Source code |
| mean_centering_per_study | Source code |
| multi.stat | Man page Source code |
| myFastList | Source code |
| mz_tolerance | Source code |
| new_adduct_mzlist | Source code |
| ot.helmert | Source code |
| overlap_ratio | Source code |
| parseFisher | Man page Source code |
| parseTukey | Man page Source code |
| perf.splsda | Source code |
| performMB | Man page Source code |
| plotGraph | Source code |
| plotProfile | Man page |
| plotVennDiagram | Source code Source code |
| plt2fig | Source code |
| predict.spls | Source code |
| qc.boxplot | Source code |
| qc.pcaplot | Source code |
| rda2list | Man page Source code |
| rectUnique | Man page Source code |
| rescale2NewRange | Source code |
| saveNetworkInSIF | Source code |
| scale.function | Source code |
| scale_vec_colours | Source code |
| searchCompLib | Source code |
| selectVar | Source code |
| setRendAttrs | Source code |
| soft_thresholding_L1 | Source code |
| sparse.mint.block_iteration | Man page Source code |
| sparsity | Source code |
| splsda | Man page Source code |
| squeezeVar | Source code |
| stratified.subsampling | Source code |
| study_split | Source code |
| sum.na | Source code |
| sumSquare | Source code |
| sumlog | Source code |
| sync2vecs | Source code |
| template.match | Man page Source code |
| trigammaInverse | Source code |
| usr2dev | Source code |
| usr2plt | Source code |
| usr2png | Man page Source code |
| var.na | Source code |
| xytrans | Source code |
| xytrans2 | Source code |
