xia-lab/MetaboAnalystR3.0
An R Package for Comprehensive Analysis of Metabolomics Data

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Vignettes
Functions
1631
Source code
62
Man pages
549
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xia-lab/MetaboAnalystR3.0: An R Package for Comprehensive Analysis of Metabolomics Data
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API

API for xia-lab/MetaboAnalystR3.0
An R Package for Comprehensive Analysis of Metabolomics Data

Global functions
.aggregateMethod2int Source code
.applyRtAdjToChromPeaks Source code
.applyRtAdjustment Source code
.compute.mummichog.RT.fgsea Man page Source code
.compute.mummichog.fgsea Man page Source code
.compute.mummichogRTSigPvals Source code
.compute.mummichogSigPvals Source code
.emptyscan.remove Man page Source code
.errorF Source code
.feature_values Source code
.get.mSet Source code
.getChromPeakData Source code
.getDdaMS2Scans Source code
.getPeakGroupsRtMatrix Source code
.graph.eda Source code
.graph.noa Source code
.graph.sif Source code
.groupval Source code
.heckbert.nicenum Source code
.init.Permutations Man page Source code
.init.RT.Permutations Man page Source code
.my.slowreaders Source code
.narrow_rt_boundaries Source code
.peakIndex Source code
.perform.mummichogPermutations Source code
.perform.mummichogRTPermutations Source code
.performIntegPathMergeP Source code
.performPathEnrich Source code
.performWeightedZtest Source code
.preparePhenoListSeeds Source code
.rawMat Source code
.read.metaboanalyst.lib Man page Source code
.readDataTable Man page Source code
.search.compoundLib Source code
.set.mSet Source code
.setup.psea.library Source code
.similarityF Source code
ANCOVA 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
C_imodwt_r Man page Source code
C_modwt_r 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
ComputeMummichogRTPermPvals Source code
ComputeSubnetStats Source code
ContainInfiniteTT Source code
ContainInfiniteVolcano Source code
ContainNewSamples Source code
Convert2Dictionary Source code
Convert2Mummichog Man page 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
Densitygrouping_slave Man page Source code
EBAM.Init Man page Source code
ExcludeNodes Source code
ExperimentsCluster_doe Man page 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
GetDefaultRTTol Source code
GetDefaultSPLSCVComp Source code
GetDefaultSPLSPairComp Source code
GetEBAMSigColNames Source code
GetEBAMSigMat Source code
GetEBAMSigRowNames Source code
GetEBAMSuggestedA0 Source code
GetECMsg 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
GetPeakFormat 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
MSW.extendLength Source code
MSW.extendNBase Source code
MSW.getLocalMaximumCWT Source code
MSW.getRidge 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
MatchQueryOnKEGGMap Source code
MeanCenter Source code
MedianNorm Source code
MergeDatasets Man page Source code
MergeDuplicates Man page Source code
MetaboAnalystR Man page
MetaboliteMappingExact Man page Source code
Noise_evaluate Man page
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
PeakPicking_MatchedFilter_slave Man page Source code
PeakPicking_centWave_slave Man page Source code
PeakPicking_core Man page Source code
PeakPicking_prep Man page 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
PerformDataInspect Man page Source code
PerformDataNormalization Source code
PerformDataTrimming Man page 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
PerformMSDataOutput 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
PerformParamsOptimization Man page Source code
PerformPeakAlignment Man page Source code
PerformPeakAnnotation Man page Source code
PerformPeakFiling Man page Source code
PerformPeakGrouping Man page Source code
PerformPeakPicking 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
Plot.sampletrend 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
QC_RLSC 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
RT.Adjust_Slave Man page Source code
RUV_2 Source code
RUV_random Source code
RUVg_cor Source code
RUVr_cor Source code
RUVs_cor 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
SaveRCommands 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
SetPlotParam 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
SetupRSclient Source code
SetupSMPDBLinks Man page Source code
ShowMemoryUse Source code
SlaveCluster_doe Man page Source code
Statistic_doe Man page Source code
SumNorm Man page Source code
Ttests.Anal Man page Source code
UnzipUploadedFile Man page Source code
UpdateData Man page Source code
UpdateEC_Rules 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
WaveICA Source code
XSet2MSet Man page Source code
add_data Source code
add_markers Source code
add_trace Man page Source code
analyze.lipids Man page Source code
annotateGrp 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
as_widget Source code
attachList Source code
binYonX Source code
breaks_on_nBins Source code
calcCV Man page Source code
calcCiS Source code
calcGaussianS Man page Source code
calcGseaStat2 Source code
calcIsotopeMatrix Source code
calcMaximumCarbon Source code
calcPC.hcs Source code
calcPPS2 Man page Source code
calcRCS_GSValues Man page Source code
calculateConcISO Man page Source code
calculateConcNoISO Source code
calculateGPRT Man page
calculateGPRT_old Source code
calculatePPKs Man page Source code
calculateSet_doe Man page Source code
checkHypothese Source code
checkIntensitiesAtRtBoundaries Source code
checkIps Source code
checkIsotopes Source code
checkNormalDistribution Source code
checkOidCausality Source code
checkParams Source code
checkQuasimolion Source code
checkSinusDistribution Source code
cleanMem Source code
color_scale Source code
combat Source code
combineParams Source code
combinePvals Source code
community.significance.test Source code
computeConc Man page Source code
concplot Source code
config Source code
continuousPtsAboveThreshold Source code
continuousPtsAboveThresholdIdx Source code
convert2JsonList Source code
convertIgraph2JSON Source code
convertPNG2PDF Source code
count_cpd2mz Source code
creatPeakTable Man page Source code
create.matrix Source code
createCVset Man page Source code
createHypothese Source code
createModel Source code
decode Source code
decodeAll Source code
defl.select Source code
deflation Source code
dependency_dir Source code
descendMin Source code
descendMinTol Source code
descendZero Source code
doCompoundMapping Man page 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
encode Source code
end.with Source code
estimatePPM Source code
estimateSNThresh Source code
expand.grid.subset Source code
explained_variance Source code
fgsea2 Man page Source code
fig2dev Source code
fillpathways Man page Source code
filterPeaksfromNoise Source code
filterPpmError Source code
filtfft Source code
findAdducts Source code
findEqualGreaterM Source code
findIsotopes.CAMERA Source code
findIsotopes.IPO Source code
findIsotopesPspec Source code
findTruePeaks 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
getAllPeakEICs Source code
getBestHit Source code
getCcdParameter Source code
getClusterType Source code
getDataFromTextArea Man page Source code
getEIC4Peaks Source code
getEICs Source code
getEdgeLabel Source code
getEdgeLty Source code
getFactorSize Source code
getIdx Source code
getIntensitiesFromRawdata Source code
getIsotopeCluster Source code
getLayout Source code
getLocalNoiseEstimate Source code
getMaxSettings Source code
getMaximumLevels Source code
getPeaklist Source code
getPeaks_selection Source code
getRGTVValues Source code
getVennCounts Source code
getderivativeIons Source code
getndp Source code
groupval 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
imputeLinInterpol Source code
internal_predict.DA Source code
internal_wrapper.mint Source code
is.wholenumber Source code
isEmptyMatrix Man page Source code
is_blank Source code
joinOverlappingPeaks Source code
kwtest Man page Source code
l2.norm Source code
layout Source code
layout.matrix Source code
layout.plotly Source code
layout.shiny.tag.list 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
mSet2xcmsSet Man page Source code
make_cpdlib Man page Source code
make_cpdlist Man page Source code
make_ecpdlist Man page Source code
map Man page
massDiffMatrix Source code
matrix.cov Source code
mb.1D Source code
mb.2D Source code
mean_centering_per_study Source code
modify_list Source code
multi.stat Man page Source code
myFastList Source code
mz.trim_random Man page Source code
mz.trim_specific Man page Source code
mz_tolerance Source code
na.flatfill Source code
naOmit Source code
new_adduct_mzlist Source code
new_id Source code
optimize.xcms.doe Man page Source code
optimizxcms.doe.peakpicking Man page Source code
ot.helmert Source code
overlap_ratio Source code
parseFisher Man page Source code
parseTukey Man page Source code
peaks_IPO Source code
peakwidth_est Source code
percentOutput Source code
perf.splsda Source code
performMB Man page Source code
plot.MS_3D Man page Source code
plotContours Source code
plotGraph Source code
plotProfile Man page
plotVennDiagram Source code Source code
plot_ly Source code
plotlyHtmlwidgetsCSS Source code
plotlyMainBundle Source code
plotly_build Source code
plotly_build.NULL Source code
plotly_build.gg Source code
plotly_build.list Source code
plotly_build.plotly Source code
plt2fig Source code
predict.spls Source code
qc.boxplot Source code
qc.pcaplot Source code
rda2list Man page Source code
read.InMemMSd.data Source code
read.MSdata Source code
read.OnDiskMS.data Source code
readLists Source code
rectUnique Source code
rescale2NewRange Source code
resultIncreased_doe Man page Source code
rt.trim_random Man page Source code
rt.trim_specific Man page Source code
sampclass Source code
saveNetworkInSIF Source code
scale.function Source code
scale_vec_colours Source code
searchCompLib Source code
selectVar Source code
setDefaultLists 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
ssm_trim Man page 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
testNormalDistribution Source code
testSinusDistribution Source code
to_JSON Source code
trigammaInverse Source code
trimm Source code
typeCastParams Source code
typedArrayPolyfill Source code
updateRawSpectraParam Man page
usr2dev Source code
usr2plt Source code
usr2png Man page Source code
var.na Source code
xytrans Source code
xytrans2 Source code
xia-lab/MetaboAnalystR3.0 documentation built on May 6, 2020, 11:03 p.m.

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