Man pages for xia-lab/MetaboAnalystR
An R Package for Comprehensive Analysis of Metabolomics Data

AddErrMsgAdds an error message
analyze.lipidsLipid analysis pipeliner
ANOVA2.AnalPerform Two-way ANOVA
ANOVA.AnalPerform ANOVA analysis
aofANOVA
aov.1wayrepPerform Two-way ANOVA
aov.2wayPerform Two-way ANOVA
aov.mixedPerform Two-way ANOVA
ASCAfun1Function to perform ASCA Adapted from online R script with...
ASCAfun2Function to perform ASCA
ASCAfun.resFunction to perform ASCA
calculateConcISOCalculate Concentration ISO
CalculateFeatureRankingCalculates feature importance
CalculateGlobalTestScoreQuantitative enrichment analysis with globaltest
CalculateHyperScoreOver-representation analysis using hypergeometric tests
CalculateImpVarCutoffCalculate the Important Variable Cutoff
CalculateOraScoreCalculate ORA score
CalculatePairwiseDiffCalculate Pairwise Differences
CalculateQeaScoreCalculate quantitative enrichment score
CalculateSSPSingle sample profiling to compare with
CentroidCheckCentroidCheck
CheckMetaDataConsistencyCheck if data are ready for meta-analysis
CleanDataPerform data cleaning
CleanDataMatrixClean the data matrix
CleanNumberReplace infinite numbers
ClearStringsRemove spaces
ComputeAverageCurveCompute average ROC curve
computeConcLipid analysis
ComputeHighLowCompute the 95 percent interval for threshold ROC
ContainMissingCheck for missing data
Convert2MummichogConvert mSetObj to proper format for MS Peaks to Pathways...
Convert2MummichogMetaPathConvert mSetObj to proper format for MS Peaks to Pathways...
CovariateScatter.AnalCovariateScatter.Anal
CreateAnalNullMsgCreate null message for analysis Creates a message for the...
CreateANOVAdocCreate report of analyses
CreateAOV2docCreate report of analyses
CreateASCAdocCreate report of analyses
CreateBiomarkerInputDocCreate biomarker analysis report: Data Input
CreateBiomarkerIntrCreate biomarker analysis report: Introduction
CreateBiomarkerOverviewCreate biomarker analysis report: Overview
CreateBiomarkerRatioOverviewCreate biomarker analysis report: Normalization, ratio
CreateBiomarkerRnwReportCreate report of analyses (Biomarker)
CreateCorAnalysisCreate report of analyses
CreateCorHeatmapCreate report of analyses
CreateCorrDocCreate report of analyses
CreateCovAdjCreate report of analyses
createCVsetSeparate data set using k-fold cross validation (CV)
CreateEBAMdocCreate report of analyses
CreateEnrichAnalDocCreate report of analyses (Met Enrichment)
CreateEnrichInputDocCreate report of analyses (Met Enrichment)
CreateEnrichIntrCreate report of analyses (Met Enrichment)
CreateEnrichORAdocCreate report of analyses (Met Enrichment)
CreateEnrichOverviewCreate report of analyses (Met Enrichment)
CreateEnrichProcessDocCreate report of analyses (Met Enrichment)
CreateEnrichQEAdocCreate report of analyses (Met Enrichment)
CreateEnrichRnwReportCreate report of analyses (Met Enrichment)
CreateEnrichSSPdocCreate report of analyses (Met Enrichment)
CreateFooterCreate report of analyses (Met Enrichment)
CreateGraphCreate igraph from the edgelist saved from graph DB and...
CreateGSEAAnalTableCreate Mummichog report of analyses
CreateHCdocCreate report of analyses
CreateIntegMatchingTableCreateIntegMatchingTable
CreateIntegPathwayAnalysisRnwReportCreate report of analyses (IntegPathwayAnalysis)
CreateIntegratedPathwayAnalInputDocCreate integrated pathway report: Data Input
CreateIntegratedPathwayAnalIntrCreate integrated pathway analysis report: Introduction
CreateIntegratedPathwayDocCreate integrated pathway analysis report
CreateIntegratedPathwayGeneMapTableCreate a x-table for gene name mapping
CreateIntegratedPathwayNameMapTableCreate a x-table for compound name mapping
CreateIntegratedPathwayResultsTableCreate a x-table for pathway results
CreateiPCAdocCreate report of analyses
CreateKMdocCreate report of analyses
CreateLadderR-code for R-SVM
CreateMappingResultTableCreates the mapping result table
CreateMBdocCreate report of analyses
CreateMetaAnalTableCreate Mummichog report of analyses
CreateMetaAnalysisDEdocCreate MetaAnalysis analysis report: Data Normalization
CreateMetaAnalysisInputDocCreate MetaAnalysis analysis report: Data Input
CreateMetaAnalysisIntrCreate MetaAnalysis analysis report: Introduction
CreateMetaAnalysisNORMdocCreate MetaAnalysis analysis report: Data Normalization
CreateMetaAnalysisOutputCreate MetaAnalysis analysis report: Data Normalization
CreateMetaAnalysisOverviewCreate MetaAnalysis analysis report: Overview
CreateMetaAnalysisRnwReportCreate report of analyses (Meta-Analysis)
CreateMetaMummichogInputDocCreate analysis report: Functional Meta-Analysis Data Input
CreateMetaMummichogIntroCreate analysis report: Functional Meta-Analysis Introduction
CreateMetaMummichogResultsCreate analysis report: Functional Meta-Analysis Results
CreateMetaOverviewCreate report of analyses
CreateMetaPathRnwReportCreate report of analyses (Biomarker)
CreateMetaTableCreate MetaAnalysis table of results
CreateModelBiomarkersDocCreate biomarker analysis report: ROC Curve Based Model...
CreateMultiBiomarkersDocCreate biomarker analysis report: Multivariate Biomarker...
CreateMummichogAnalTableCreate Mummichog report of analyses
CreateMummichogAnalysisDocCreate mummichog analysis report
CreateMummichogInputDocCreate Mummichog analysis report: Data Input
CreateMummichogIntroCreate mummichog analysis report: Introduction
CreateMummichogLibsCreate Mummichog Libraries from KEGG
CreateMummichogMetaAnalPathTableCreate analysis report: Functional Meta-Analysis Results...
CreateMummichogMetaAnalReportCreate analysis report: Functional Meta-Analysis
CreateMummichogOverviewCreate Mummichog analysis report: Overview
CreateMummichogRnwReportCreate report of analyses (Biomarker)
CreateNetworkExplorerDocCreate integrated pathway analysis report
CreateNetworkExplorerInputDocCreate network explorer: Data Input
CreateNetworkExplorerIntrCreate integrated pathway analysis report: Introduction
CreateNetworkExplorerOverviewCreate network explorer report: Overview
CreateNetworkExplorerRnwReportCreate report of analyses (Network Explorer)
CreateNetworkGeneMapTableCreate a x-table for gene name mapping
CreateNetworkNameMapTableCreate a x-table for compound name mapping
CreateNORMdocCreate report of analyses
CreateOPLSDAdocCreate report of analyses
CreatePathAnalDocCreate report of analyses (Met Pathway)
CreatePathInputDocCreate report of analyses (Met Pathway)
CreatePathIntrCreate report of analyses (Met Pathway)
CreatePathProcessDocCreate report of analyses (Met Pathway)
CreatePathResultDocCreate report of analyses (Met Pathway)
CreatePathRnwReportCreate report of analyses (Met Pathway)
CreatePCAdocCreate report of analyses
CreatePLSdocCreate report of analyses
CreatePowerAnalDocCreate power analysis report: Power Analysis
CreatePowerInputDocCreate power analysis report: Data Input
CreatePowerIntrCreate power analysis report: Introduction
CreatePowerOverviewCreate power analysis report: Overview
CreatePowerParametersDocCreate power analysis report: Power Parameter Selection
CreatePowerRnwReportCreate report of analyses (Power)
CreateRandomForestCreate report of analyses
CreateRatioTableCreate report of analyses
CreateRawAnalysisRnwReportCreate report for raw spectra module
CreateRFdocCreate report of analyses
CreateRHistAppendixCreate report of analyses
CreateROCLabelsTableCreate a x-table for newly classified samples
CreateSAMdocCreate report of analyses
CreateSemiTransColorsCreate semitransparant colors
CreateSOMdocCreate report of analyses
CreateSPLSDAdocCreate report of analyses
CreateStatIntrCreate report of analyses
CreateStatIOdocCreate report of analyses
CreateStatRnwReportCreate report for statistical analysis module
CreateSummaryTableCreate report of analyses
CreateSVMdocCreate report of analyses
CreateTimeSeriesAnalNullMsgCreate null analysis message for time-series sweave report
CreateTimeSeriesIOdocCreate report of analyses (Met Pathway)
CreateTimeSeriesRnwReportCreate report of analyses (Met Pathway)
CreateUnivarBiomarkersDocCreate power analysis report: Biomarker Univariate Analysis
CreateUNIVdocCreate report of analyses
CreateUnivROCTableCreate summary table for univariate ROC analysis
CreateVennMetaTableCreate MetaAnalysis table of results for Venn Diagram
CrossReferencingVarious functions for mapping b/w names & database...
descendMinPerform utilities for peak grouping
doCompoundMappingPerform compound mapping
doGeneIDMappingConvert different gene IDs into entrez IDs for downstream...
doKEGG2NameMappingPerform KEGG to compound name mapping
doKOFilteringUtility function
doLogisticRegMdlDevelop a Logistic Regression Model with all of the combined...
dot-do.CVTest.LRmodelCalculate ROC performance with CV An internal function called...
dot-get.my.libRead RDS files from the internet
dot-readDataTableRead data table
EBAM.InitFor EBAM analysis
FC.AnalFold change analysis, unpaired
FeatureCorrelationPattern hunter
FilterVariableMethods for non-specific filtering of variables
findEqualGreaterMPerform utilities for peak grouping
FisherLSDFisher for ANOVA
GeneratePeakListGeneratePeakList
GetAbundanceLabelDetermine value label for plotting
GetAccuracyInfoExport biomarker accuracy information
GetAllDataNamesGet all meta-analysis name data
GetAllKMClusterMembersK-means analysis - cluster
GetAllSOMClusterMembersSOM analysis
Get.asca.tssFunction for ASCA permutation
Get.bwssCompute within group and between group sum of squares...
GetCandidateListGet all candidate compound names for a given index
GetCircleInfoExport information about selected circle
GetCIsGet confidence intervals
GetCMDRetrieve last command from the Rhistory.R file
GetCompoundDetailsFunction to get adduct details from a specified compound
Get.ConcRefGet the concentration reference
GetConvertFullPathPerform utilities for cropping images
getDataFromTextAreaTransform two column text to data matrix
GetExtendRangeExtend axis
GetFCUsed by higher functions to calculate fold change
GetFeatureNumbersNumbers for subset selection
GetFinalNameMapReturn the final (after user selection) map as dataframe
GetFisherPvalueGet fisher p-values
GetGroupNamesGet all group names
GetHTMLMetSetGiven a metset inx, return hmtl highlighted metset cmpds and...
GetHTMLPathSetGiven a metset inx, return hmtl highlighted pathway cmpds
GetImpFeatureMatGet important feature matrix
GetKEGGNodeInfoRetrieves KEGG node information
GetKMClusterMembersK-means analysis - cluster
GetLassoFreqsCompute lasso frequency
Get.LeverageFast leverage calculation for permutation purpose
GetLimmaResTableGet result table from eBayes fit object
GetMapTableGet mapping table
GetMaxPCACompFor plotting PCA, selects max top 9 components
GetMeanROCCompute data points on the ROC curve
GetMetaResultMatrixSingle.type return logFC or p value for individual data...
GetMetSetNameGiven a metset inx, give its name
GetMsetLibCheckMsgGet the library check messages
GetMsetNamesReturn the selected metset library to java for display
GetMummichogPathSetDetailsFunction to get compound details from a specified pathway
GetNetworkGeneMappingResultTableExports Gene-Mapping result into a table
GetNewSampleNamesObtain sample names and their class labels
GetNMDRStudyFunction to retrieve dataset from the Metabolomics Workbench.
GetORA.pathNamesExport pathway names from ORA analysis
GetORA.smpdbIDsOnly for human pathways (SMPDB)
GetORATableGet ORA table
Get.pAUCCalculate partial area under ROC curve
Get.predGet predicted class probability
GetQEA.keggIDsOnly for human pathways (KEGG)
GetQEA.pathNamesExport pathway names from QEA analysis
GetQEATableQEA table
GetRCommandHistoryExport R Command History
GetRFConfMatRandom Forest Confusion Matrix
GetRFConf.TableClassification performance table for random forest analysis
GetRFOOBRandom Forest OOB
GetRFSigMatRandom Forest Significance matrix
GetROC.coordsReturn ROC corodinates with confidence intervals
GetROCLassoFreqGet p-values from lasso
GetROCTtestPGet p-values for ROC
Get.rpart.summaryGet the text description of a recursive partitioning (rpart)...
GetSampleSizeLadderRetrieve sample size ladder
GetSigTableCreate Latex table
GetSigTable.AnovaSig Table for Anova
GetSigTable.Aov2Sig table for AOV2
GetSigTable.ASCATable of features well modelled by ASCA
GetSigTable.CorrSig table for Correlation Analysis
GetSigTable.DoseSig Table for Anova
GetSigTable.EBAMSig table for EBAM
GetSigTable.FCSig Table for Fold-Change Analysis
GetSigTable.MBSig table for MB analysis
GetSigTable.RFSig table for random forest analysis
GetSigTable.SAMSig table for SAM
GetSigTable.SVMSig table for SVM
GetSigTable.TTSig Table for T-test Analysis
GetSigTable.VolcanoSig table for Volcano Analysis
GetSOMClusterMembersSOM analysis
GetSSPTableReplace the last column of the ssp.mat with the final...
GetSuggestedSAMDeltaFor SAM analysis
GetSVMSigMatRecursive Support Vector Machine (R-SVM) Significance Measure
GetTopInxVolcano indices
GetTrainTestSplitMatMake random partitions
GetTtestResRetrieve T-test p-values
GetTTSigMatT-test matrix
GetUnivReportUtility method to perform the univariate analysis...
GetVariableLabelDetermine variable label for plotting
Get.VIPCalculate variable importance of projection (VIP) score for...
GetXYClusterDetermine row/column number for plotting
GroupPeakListGroup peak list
heckbertHeckbert algorithm
HMDBID2KEGGIDGiven a vector of HMDBIDs, return a vector of KEGG IDs
HMDBID2NameGiven a vector of HMDBIDs, return a vector of HMDB compound...
ImputeMissingVarData processing: Replace missing variables
InitDataObjectsConstructs a dataSet object for storing data
InitializaPlanInitializePlan
InitMSObjectsInitMSObjects
InitPowerAnalFunction for power analysis
InitStatAnalModeIntroduction for statistical analysis module report...
InitTimeSeriesAnalCreate report of analyses (Met Pathway)
iPCA.AnalPerform PCA analysis, prepare file for interactive...
isEmptyMatrixSig table matrix is empty
IsSmallSmplSizeCheck if the sample size is small
KEGGID2HMDBIDGiven a vector of KEGGIDs, return a vector of HMDB ID
KEGGID2NameGiven a vector containing KEGGIDs, returns a vector of KEGG...
KEGGPATHID2SMPDBIDsGiven a vector containing KEGG pathway IDs, return a vector...
Kmeans.AnalK-means analysis
kwtestKruskal-Wallis
ListNMDRStudiesFunction to retrieve all available datasets from the...
LoadKEGGKO_libUtility function for PerformKOEnrichAnalysis_KO01100
LogNormColumn-wise Normalization
make_cpdlistUtility function to create compound lists for permutation...
make_ecpdlistUtility function to create compound lists for permutation...
mapsPLS-DA Map
MapCmpd2KEGGNodesUtility function for PrepareKeggQueryJson
MapKO2KEGGEdgesUtility function for PrepareKeggQueryJson
Match.PatternMatch pattern for correlation analysis
meltmelt Convert an object into a molten data frame. This...
MergeDatasetsUtility function for PrepareKeggQueryJson
MergeDuplicatesMerge duplicated columns or rows by their mean
MetaboAnalystRMetaboAnalystR: A package for computating the notorious bar...
MetaboliteMappingExactMapping from different metabolite IDs
MetaPathNormalizationMetaPathNormalization
multi.statGet multiple category statistics
my.lsd.testCalculate Fisher's Least Significant Difference (LSD)
my.parse.peaklistmy.parse.peaklist
NormalizationNormalization
OPLSDA.PermutPerform OPLS-DA permutation
OPLSR.AnalPerform OPLS-DA
parseFisherReturn only the signicant comparison names
parseTukeyReturn only the signicant comparison names
PCA.AnalPerform PCA analysis
PCA.FlipRotate PCA analysis
PCA.GENESObtain principal components into a matrix that has more...
PerformAdductMappingPerformAdductMapping
PerformApproxMatchPerform approximate compound matches
Perform.ASCAPerform ASCA
Perform.ASCA.permutePerform ASCA model validation by permutation
PerformBatchCorrectionBatch Effect Correction
PerformCmpdMappingPerform compound mapping for integrative analysis methods
PerformCurrencyMappingMap currency metabolites to KEGG & BioCyc
PerformCV.explorePerform Monte-Carlo Cross Validation (MCCV)
PerformCV.testPerform MCCV for manually selected features
PerformDataInspectPerformDataInspect
PerformDataTrimmingPerform ROI Extraction from raw MS data (PerformDataTrimming)
PerformDetailMatchPerform detailed name match
PerformEachDEAnalPerforms differential expression analysis on individual data
PerformGeneMappingPerform integrated gene mapping
PerformIndNormalizationPerform normalization for individually-uploaded datasets for...
PerformIntegPathwayAnalysisPerform integrative pathway analysis
PerformKOEnrichAnalysis_KO01100Performs KO enrichment analysis based on the KO01100 map
PerformKOEnrichAnalysis_ListUtility function for PerformKOEnrichAnalysis_KO01100
PerformLimmaDEPerform differential expression analysis using Limma for...
PerformMapping_ko01100Utility function for PrepareKeggQueryJson geneIDs is text one...
performMBTimecourse analysis
PerformMetaMergeMeta-Analysis Method: Direct merging of datasets
PerformMetaPSEAPerformMetaPSEA Function to perform peak set enrichment...
performMS2searchBatchperformMS2searchBatch
performMS2searchSingleperformMS2searchSingle
PerformMultiMatchPerform multiple name matches
PerformParamsOptimizationPerform Parameters Optimization
PerformPeakProfilingPerformPeakProfiling
Perform.PermutPerform permutation tests only for ROC Tester
Perform.permutationPermutation
PerformPowerProfilingPerform power profiling
PerformPSEAFunction to perform peak set enrichment analysis
PerformPvalCombinationMeta-Analysis Method: Combining p-values
PerformROIExtractionPerform ROI Extraction from raw MS data (PerformDataTrimming)
PerformSignalDriftCorrectionSignal Drift Correction
Perform.UnivROCPerform Classical Univariate ROC
PerformVoteCountingMeta-Analysis Method: Vote Counting
PlotAccuracyPlot classification performance using different features for...
PlotANOVAPlot ANOVA
PlotANOVA2Plot Venn diagram of ANOVA results
PlotAscaImpVarPlot the important variables for each factor
PlotASCAModelPlot score plots of each ASCA model for component 1 against...
PlotASCA.PermutationPlot ASCA permutation
PlotClustPCAPlot K-means summary PCA plot
PlotCmpdSummaryPlot compound summary change to use dataSet$proc instead of...
PlotCmpdViewPlot Compound View
PlotConcRangePlot the compound concentration data compared to the...
PlotCorrPattern hunter, correlation plot
PlotCorrHeatMapPattern hunter, corr heatmap
PlotDetailROCPlot detailed ROC
plot_distBatch Distance Plotting
PlotEBAM.CmpdPlot EBAM
PlotEnrichDotPlotPlot MSEA Dot Plot
PlotEnrichNet.OverviewPlotEnrichNet.Overview
PlotEnrichPieChartCreate a pie chart for compound classes
PlotFCPlot fold change
PlotHCTreePlot Dendrogram
PlotHeatMapCreate Heat Map Plot
PlotHeatMap2Plot heatmap visualization for time-series data
PlotImpBiomarkersPlot selected compounds by their percentage frequency
PlotImpVarPlot PLS important variables,
PlotImpVarMetaPlot PLS important variables,
PlotInmexGraphPlot an igraph object and return the node information...
PlotInmexPathPlot integrated methods pathway analysis
PlotInteractionPlot ASCA interaction plots
PlotKEGGPathPlot metabolome pathway
PlotKmeansPlot K-means analysis
PlotMBTimeProfilePlot MB Time Profile
PlotMetaCorrHeatmapGenerate correlation heatmap for metadata
PlotMetaHeatmapGenerate heatmaps for metadata table
PlotMetpaPathPlot KEGG pathway
plotMirrorplotMirror
PlotModelScreePlot scree plots for each model in ASCA
PlotMSEA.OverviewPlot MSEA overview
plotMSfeatureplotMSfeature
PlotMultiFacCmpdSummaryPlot compound summary for multi-linear regression tool
PlotNormSummaryTwo plot summary plot: Feature View of before and after...
PlotOPLS2DScoreCreate OPLS-DA score plot
PlotOPLS.ImpPlotOPLS.Imp OPLS VIP plotting function
PlotOPLS.MDLPlot OPLS
PlotOPLS.PermutationPlot OPLS-DA permutation
PlotOPLS.SplotS-plot for OPLS-DA
PlotORAPlot over-representation analysis (ORA)
PlotPathSummaryPlot a scatterplot (circle) overview of the matched pathways
PlotPathwayMetaAnalysisPlotPathwayMetaAnalysis
PlotPCA2DScoreCreate 2D PCA score plot
PlotPCA3DLoadingPlotPCA3DLoading
PlotPCA3DScoreCreate 3D PCA score plot
PlotPCA3DScoreImgCreate 3D PCA score plot
PlotPCABiplotCreate PCA Biplot, set xpd = T to plot outside margin
PlotPCALoadingPlot PCA loadings and also set up the matrix for display
PlotPCA.overviewScatter plot colored by different batches
PlotPCAPairSummaryPlot PCA pair summary, format image in png, tiff, pdf, ps,...
PlotPCAScreePlot PCA scree plot
PlotPeaks2PathsPlotPeaks2Paths
Plot.PermutationPlot results of permutation tests
PlotPLS2DScorePlot PLS score plot
PlotPLS3DLoadingPlotPLS3DLoading
PlotPLS3DScorePlot PLS 3D score plot
PlotPLS3DScoreImgPlot PLS 3D score plot
PlotPLS.ClassificationPlot PLS-DA classification performance using different...
PlotPLS.ImpPlot PLS important features
PlotPLSLoadingPlot PLS loading plot, also set the loading matrix for...
PlotPLSPairSummaryPlot PLS pairwise summary
PlotPLS.PermutationPlot PLS-DA classification performance using different...
PlotPowerProfilePlot power profile
PlotPowerStatPlot power statistics
PlotProbViewPlot a summary view of the classification result
PlotProbViewTestPlot a summary view of the classification result of tester...
plotProfilePlot the variable across time points (x)
PlotPSEAIntegPathsPlotPSEAIntegPaths
PlotQEA.MetSetView individual compounds related to a given metabolite set
PlotQEA.OverviewPlot QEA overview
PlotRF.ClassifyPlot Random Forest
PlotRF.ClassifyMetaPlot Random Forest
PlotRF.OutlierPlot Random Forest outliers
PlotRF.VIPPlot Random Forest variable importance
PlotRF.VIPMetaPlot Random Forest variable importance
PlotROCPlot ROC
PlotROC.LRmodelPlot ROC for the logistic regression model
PlotROCTestPlot ROC for the ROC Curve Based Model Creation and...
PlotRocUnivBoxPlotPlot a boxplot view of a selected compound
PlotRSVM.ClassificationRecursive Support Vector Machine (R-SVM) plot
PlotRSVM.CmpdRecursive Support Vector Machine (R-SVM) plot of important...
PlotSAM.CmpdPlot SAM
PlotSAM.FDRPlot SAM Delta Plot
PlotSampleNormSummaryTwo plot summary plot: Sample View of before and after...
Plot.sampletrendSample Trend Scatter
PlotSelectedFeatureCreate a box-plot of a feature's expression pattern across...
PlotSigVarSupporting function for plotting important variables for each...
plotSingleTICplotSingleTIC
PlotSOMSOM Plot
PlotSPLS2DScoreScore Plot SPLS-DA
PlotSPLS3DLoadingPlotSPLS3DLoading
PlotSPLS3DScore3D SPLS-DA score plot
PlotSPLS3DScoreImgPlot sPLS-DA 3D score plot
PlotSPLSDA.ClassificationCreate SPLS-DA classification plot
PlotSPLSLoadingCreate SPLS-DA loading plot
PlotSPLSPairSummaryPlot SPLS-DA
PlotStaticCorrHeatMapCreate high resolution static HeatMap for download only
PlotStaticHeatMapCreate high resolution static HeatMap for download only
PlotStaticHeatMap2Create high resolution static HeatMap for download only
PlotStaticMetaHeatmapCreate high resolution static HeatMap for download only
PlotSubHeatMapCreate Sub Heat Map Plot
PlotTestAccuracyPlot classification performance using different features for...
PlotTTPlot t-test
PlotVolcanoCreate volcano plot
PlotXICPlotXIC
PLSDA.CVPLS-DA classification and feature selection
PLSDA.PermutPerform PLS-DA permutation
PLSR.AnalPLS analysis using oscorespls (Orthogonal scores algorithm)...
Predict.classGet predicted class probability
PrepareIntegDataPrepare integrated data
PrepareKeggQueryJsonPrepare user's query for mapping KEGG Global Metabolic...
PrepareMetaPathPrepareMetaPath
PrepareNetworkDataPrepare data for network exploration
PreparePDFReportCreate report of analyses
PreparePeakTable4PSEAPreparePeakTable4PSEA
PreparePermResultPrepare report for permutation tests
PreparePrenormDataPrepare data for normalization
PrepareROCDataPrepare data for ROC analysis
PrepareROCDetailsROC with CI for AUC
PrepareUpsetDataPrepare data for Upset diagram
processMSMSuploadprocessMSMSupload
RankFeaturesRank features based on different importance measures
Read.BatchDataBCData I/O for batch effect checking
Read.BatchDataTBData I/O for batch effect checking
ReadIndDataRead in individual data
ReadMetaDataReadMetaData
ReadMetaPathTableReadMetaPathTable
ReadMetaPathTableMixReadMetaPathTableMix
Read.mzTabRead an mzTab tab separated file from the passed in file....
ReadPairFileRead paired peak or spectra files
Read.PeakListRead peak list files
Read.PeakListDataConstructor to read uploaded user files into the mummichog...
Read.SignalDriftDataData I/O for signal drift checking
Read.TextDataRead.TextData Constructor to read uploaded CSV or TXT files...
Read.TextDataTsRead.TextDataTs
RecordRCommandRecord R Commands
rectUniquePerform utilities for peak grouping
RegisterDataRegister data in R
RemoveCmpdRemove selected compounds
RemoveDataRemove data object, the current dataSet will be the last one...
RemoveDuplicatesGiven a data with duplicates, remove duplicates
RemoveFileRemove file
RemoveFolderRemove folder
RemoveGeneRemove selected genes
RemoveMissingPercentData processing: remove variables with missing values
ReplaceMinReplace missing or zero values
RerenderMetPAGraphRedraw current graph for zooming or clipping then return a...
RF.AnalPerform Random Forest Analysis
RF.AnalMetaPerform Random Forest Analysis
ROCPredSamplesTableCreate a table of newly classified samples
RSVMR-SVM core code
RSVM.AnalRecursive Support Vector Machine (R-SVM)
SaintyCheckMSPfileSaintyCheckMSPfile
SAM.AnalPerform Signifiance Analysis of Microarrays (SAM) analysis
SanityCheckDataSanity Check Data
SanityCheckIndDataSanity check of individual datasets for meta-analysis
SanityCheckMetaSanityCheckMeta#'
SanityCheckMetaPathTableSanityCheckMetaPathTable
SanityCheckMummichogDataSanity Check Data
savePeakListMetaDataFunction to save each mSetObj as a RDS file to be used later...
SaveTransformedDataSave the processed data with class names
SearchByCompoundSearch for compound from all member compounds of metabolite...
SearchByNameGiven a metabolite set name, search its index
SearchMsetLibrariesSearch metabolite set libraries
SearchNetDBPerform mapping of user's data to interaction network
SelectMultiDataSelect one or more datasets for meta-analysis
SetAnalysisModeSet biomarker analysis mode
SetCachexiaSetUsedSet the cachexia set used
SetCandidateSet matched name based on user selection from all potential...
SetCurrentGroupsTo choose from two groups
SetCurrentMsetLibSet current user selected metset library for search
SetCustomDataSet custom data
SetDataTypeOfMetaSetDataTypeOfMeta
SetDesignTypeFor two factor time series only
setInclusionDataSetssetInclusionDataSets#'
SetKEGG.PathLibSet KEGG pathway library
SetMetabolomeFilterSet metabolome filter
setMS2DBOptsetMS2DBOpt
SetMummichogPvalSet the cutoff for mummichog analysis
SetMummichogPvalFromPercentSet the cutoff for mummichog analysis
SetOrganismSet organism for further analysis
SetPeakEnrichMethodSet the peak enrichment method for the MS Peaks to Paths...
SetPeakFormatSet the peak format for the mummichog analysis
SetPeakList.GroupValuesSet peak list group values
SetPeakParamSetPeakParam
SetRTincludedSetRTincluded
SetSMPDB.PathLibSet SMPDB pathway library
Setup.AdductDataSave adduct names for mapping
Setup.BiofluidTypeSave biofluid type for SSP
Setup.ConcDataSave concentration data
Setup.HMDBReferenceMetabolomeRead user uploaded metabolome as a list of HMDB compound...
SetupKEGGLinksOnly works for human (hsa.rda) data
Setup.KEGGReferenceMetabolomeRead user uploaded metabolome as a list of KEGG pathway ids
Setup.MapDataSave compound name for mapping
SetupSMPDBLinksOnly works for human (hsa.rda) data
Setup.UserMsetLibDataRead user upload metabolite set library file
SOM.AnalSOM analysis
sparse.mint.block_iterationPerform Sparse Generalized Canonical Correlation (sgccak)
splsdaPerform sPLS-DA
SPLSR.AnalPerform SPLS-DA
SumNormRow-wise Normalization
template.matchPattern hunter
Ttests.AnalPerform t-test analysis
UnzipUploadedFileUnzip .zip files
UpdateDataUpdate data for filtering
UpdateEC_RulesUpdate the mSetObj with user-selected parameters for MS Peaks...
UpdateGraphSettingsUpdate graph settings
UpdateInstrumentParametersUpdate the mSetObj with user-selected parameters for MS Peaks...
UpdateIntegPathwayAnalysisUpdate integrative pathway analysis for new input list
UpdateOPLS.SplotUpdate OPLS loadings
UpdatePCA.LoadingUpdate PCA loadings
UpdatePLS.LoadingUpdate PLS loadings
usr2pngPerform utilities for MetPa
Volcano.AnalPerform Volcano Analysis
XSet2MSetConverts xset object from XCMS to mSet object for...
xia-lab/MetaboAnalystR documentation built on Feb. 18, 2024, 9:13 p.m.