# An R Package for Comprehensive Analysis of Metabolomics Data

## Documentation for package ‘MetaboAnalystR’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E F G H I K L M N O P R S T U V X misc

## -- A --

AddErrMsg | Adds an error message
analyze.lipids | Lipid analysis pipeliner
ANOVA.Anal | Perform ANOVA analysis
ANOVA2.Anal | Perform Two-way ANOVA
aof | ANOVA
aov.between | Perform Two-way ANOVA
aov.repeated | Perform Two-way ANOVA
aov.within | Perform Two-way ANOVA
ASCAfun.res | Function to perform ASCA
ASCAfun1 | Function to perform ASCA
ASCAfun2 | Function to perform ASCA

## -- C --

calculateConcISO | Calculate Concentration ISO
CalculateFeatureRanking | Calculates feature importance
CalculateGlobalTestScore | Quantitative enrichment analysis with globaltest
CalculateHyperScore | Over-representation analysis using hypergeometric tests
CalculateImpVarCutoff | Perform OPLS-DA
CalculateOraScore | Calculate ORA score
CalculatePairwiseDiff | Calculate Pairwise Differences
CalculateQeaScore | Calculate quantitative enrichment score
CalculateSSP | Single sample profiling to compare with
CheckMetaDataConsistency | Check if data are ready for meta-analysis
CleanData | Perform data cleaning
CleanDataMatrix | Clean the data matrix
CleanNumber | Replace infinite numbers
ClearNegatives | Data processing: Dealing with negative values
ClearStrings | Remove spaces
ClearUserDir | Clear folder and memory
ComputeAverageCurve | Compute average ROC curve
computeConc | Lipid analysis
ComputeHighLow | Compute the 95 percent interval for threshold ROC
Convert2Mummichog | Convert mSetObj to proper format for MS Peaks to Pathways module
CreateAnalNullMsg | Create null message for analysis Creates a message for the Sweave report
CreateANOVAdoc | Create report of analyses
CreateAOV2doc | Create report of analyses
CreateASCAdoc | Create report of analyses
CreateBiomarkerInputDoc | Create biomarker analysis report: Data Input
CreateBiomarkerIntr | Create biomarker analysis report: Introduction
CreateBiomarkerOverview | Create biomarker analysis report: Overview
CreateBiomarkerRatioOverview | Create biomarker analysis report: Normalization, ratio
CreateBiomarkerRnwReport | Create report of analyses (Biomarker)
CreateCorrDoc | Create report of analyses
createCVset | Separate data set using k-fold cross validation (CV)
CreateEBAMdoc | Create report of analyses
CreateEnrichAnalDoc | Create report of analyses (Met Enrichment)
CreateEnrichInputDoc | Create report of analyses (Met Enrichment)
CreateEnrichIntr | Create report of analyses (Met Enrichment)
CreateEnrichORAdoc | Create report of analyses (Met Enrichment)
CreateEnrichOverview | Create report of analyses (Met Enrichment)
CreateEnrichProcessDoc | Create report of analyses (Met Enrichment)
CreateEnrichQEAdoc | Create report of analyses (Met Enrichment)
CreateEnrichRnwReport | Create report of analyses (Met Enrichment)
CreateEnrichSSPdoc | Create report of analyses (Met Enrichment)
CreateFooter | Create report of analyses (Met Enrichment)
CreateGraph | Create igraph from the edgelist saved from graph DB and decompose into subnets
CreateHCdoc | Create report of analyses
CreateHeatmap2doc | Create report of analyses
CreateIntegPathwayAnalysisRnwReport | Create report of analyses (IntegPathwayAnalysis)
CreateIntegratedPathwayAnalInputDoc | Create integrated pathway report: Data Input
CreateIntegratedPathwayAnalIntr | Create integrated pathway analysis report: Introduction
CreateIntegratedPathwayDoc | Create integrated pathway analysis report
CreateIntegratedPathwayGeneMapTable | Create a x-table for gene name mapping
CreateIntegratedPathwayNameMapTable | Create a x-table for compound name mapping
CreateIntegratedPathwayResultsTable | Create a x-table for pathway results
CreateiPCAdoc | Create report of analyses
CreateKMdoc | Create report of analyses
CreateLadder | R-code for R-SVM
CreateMappingResultTable | Creates the mapping result table
CreateMBdoc | Create report of analyses
CreateMetaAnalysisDEdoc | Create MetaAnalysis analysis report: Data Normalization
CreateMetaAnalysisInputDoc | Create MetaAnalysis analysis report: Data Input
CreateMetaAnalysisIntr | Create MetaAnalysis analysis report: Introduction
CreateMetaAnalysisNORMdoc | Create MetaAnalysis analysis report: Data Normalization
CreateMetaAnalysisOutput | Create MetaAnalysis analysis report: Data Normalization
CreateMetaAnalysisOverview | Create MetaAnalysis analysis report: Overview
CreateMetaAnalysisRnwReport | Create report of analyses (Meta-Analysis)
CreateMetaTable | Create MetaAnalysis table of results
CreateModelBiomarkersDoc | Create biomarker analysis report: ROC Curve Based Model Creation and Evaluation
CreateMultiBiomarkersDoc | Create biomarker analysis report: Multivariate Biomarker Analysis
CreateMummichogAnalTable | Create Mummichog report of analyses
CreateMummichogAnalysisDoc | Create mummichog analysis report
CreateMummichogInputDoc | Create Mummichog analysis report: Data Input
CreateMummichogIntro | Create mummichog analysis report: Introduction
CreateMummichogOverview | Create Mummichog analysis report: Overview
CreateMummichogRnwReport | Create report of analyses (Biomarker)
CreateNetworkExplorerDoc | Create integrated pathway analysis report
CreateNetworkExplorerInputDoc | Create network explorer: Data Input
CreateNetworkExplorerIntr | Create integrated pathway analysis report: Introduction
CreateNetworkExplorerOverview | Create network explorer report: Overview
CreateNetworkExplorerRnwReport | Create report of analyses (Network Explorer)
CreateNetworkGeneMapTable | Create a x-table for gene name mapping
CreateNetworkNameMapTable | Create a x-table for compound name mapping
CreateNORMdoc | Create report of analyses
CreateOPLSDAdoc | Create report of analyses
CreatePathAnalDoc | Create report of analyses (Met Pathway)
CreatePathInputDoc | Create report of analyses (Met Pathway)
CreatePathIntr | Create report of analyses (Met Pathway)
CreatePathProcessDoc | Create report of analyses (Met Pathway)
CreatePathResultDoc | Create report of analyses (Met Pathway)
CreatePathRnwReport | Create report of analyses (Met Pathway)
CreatePCAdoc | Create report of analyses
CreatePLSdoc | Create report of analyses
CreatePowerAnalDoc | Create power analysis report: Power Analysis
CreatePowerInputDoc | Create power analysis report: Data Input
CreatePowerIntr | Create power analysis report: Introduction
CreatePowerOverview | Create power analysis report: Overview
CreatePowerParametersDoc | Create power analysis report: Power Parameter Selection
CreatePowerRnwReport | Create report of analyses (Power)
CreateRatioTable | Create report of analyses
CreateRFdoc | Create report of analyses
CreateRHistAppendix | Create report of analyses
CreateROCLabelsTable | Create a x-table for newly classified samples
CreateSAMdoc | Create report of analyses
CreateSemiTransColors | Create semitransparant colors
CreateSOMdoc | Create report of analyses
CreateSPLSDAdoc | Create report of analyses
CreateStatIntr | Create report of analyses
CreateStatIOdoc | Create report of analyses
CreateStatRnwReport | Create report for statistical analysis module
CreateSummaryTable | Create report of analyses
CreateSVMdoc | Create report of analyses
CreateTimeSeriesAnalNullMsg | Create null analysis message for time-series sweave report
CreateTimeSeriesIOdoc | Create report of analyses (Met Pathway)
CreateTimeSeriesRnwReport | Create report of analyses (Met Pathway)
CreateUnivarBiomarkersDoc | Create power analysis report: Biomarker Univariate Analysis
CreateUNIVdoc | Create report of analyses
CreateUnivROCTable | Create summary table for univariate ROC analysis
CreateVennMetaTable | Create MetaAnalysis table of results for Venn Diagram
CrossReferencing | Various functions for mapping b/w names & database identifiers Given a list of compound names or ids, find matched name or ids from selected databases
CVTest.LRmodel | Calculate ROC performance with CV

## -- D --

descendMin | Perform utilities for peak grouping
doCompoundMapping | Perform compound mapping
doEmblProtein2EntrezMapping | Utility function for PerformNetEnrichment
doGeneIDMapping | Perform various annotation
doKEGG2NameMapping | Perform KEGG to compound name mapping
doKOFiltering | Utility function

## -- E --

EBAM.A0.Init | For EBAM analysis
EBAM.Cmpd.Init | For EBAM analysis

## -- F --

FC.Anal.paired | Fold change analysis, paired
FC.Anal.unpaired | Fold change analysis, unpaired
FeatureCorrelation | Pattern hunter
fgsea2 | Pre-ranked gsea adapted for untargeted metabolomics
FilterVariable | Methods for non-specific filtering of variables
findEqualGreaterM | Perform utilities for peak grouping
FisherLSD | Fisher for ANOVA
FormatPeakList | Format Peak List This function formats the CAMERA output to a usable format for MetaboAanlyst.

## -- G --

genLogisticRegMdl | Develop a Logistic Regression Model with all of the combined k-fold CV subsets
Get.asca.tss | Function for ASCA permutation
Get.bwss | Compute within group and between group sum of squares (BSS/WSS) for each row of a matrix which may have NA
Get.ConcRef | Get the concentration reference
Get.Leverage | Fast leverage calculation for permutation purpose
Get.pAUC | Calculate partial area under ROC curve
Get.pred | Get predicted class probability
Get.rpart.summary | Get the text description of a recursive partitioning (rpart) result
Get.VIP | Calculate variable importance of projection (VIP) score for PLS object
GetAbundanceLabel | Determine value label for plotting
GetAccuracyInfo | Export biomarker accuracy information
GetAllDataNames | Get all meta-analysis name data
GetAllKMClusterMembers | K-means analysis - cluster
GetAllSOMClusterMembers | SOM analysis
GetCandidateList | Get all candidate compound names for a given index
GetCircleInfo | Export information about selected circle
GetCIs | Get confidence intervals
GetCMD | Retrieve last command from the Rhistory.R file
GetConvertFullPath | Perform utilities for cropping images
getDataFromTextArea | Transform two column text to data matrix
GetExtendRange | Extend axis
GetFC | Used by higher functions to calculate fold change
GetFeatureNumbers | Numbers for subset selection
GetFinalNameMap | Return the final (after user selection) map as dataframe
GetFisherPvalue | Get fisher p-values
GetHTMLMetSet | Given a metset inx, return hmtl highlighted metset cmpds and references
GetHTMLPathSet | Given a metset inx, return hmtl highlighted pathway cmpds
GetImpFeatureMat | Get important feature matrix
GetKEGGNodeInfo | Retrieves KEGG node information
GetKMClusterMembers | K-means analysis - cluster
GetLassoFreqs | Compute lasso frequency
GetLimmaResTable | Get result table from eBayes fit object
GetMapTable | Get mapping table
GetMaxPCAComp | For plotting PCA, selects max top 9 components
GetMeanROC | Compute data points on the ROC curve
GetMetaResultMatrix | Single.type return logFC or p value for individual data analysis
GetMetaSigHitsTable | Export the significant hits from meta-analysis
GetMetSetName | Given a metset inx, give its name
GetMsetLibCheckMsg | Get the library check messages
GetMsetLibSearchResult | Return metset search results
GetMsetNames | Return the selected metset library to java for display
GetNetworkGeneMappingResultTable | Exports Gene-Mapping result into a table
GetNewSampleNames | Obtain sample names and their class labels
GetORA.pathNames | Export pathway names from ORA analysis
GetORA.smpdbIDs | Only for human pathways (SMPDB)
GetORATable | Get ORA table
GetQEA.keggIDs | Only for human pathways (KEGG)
GetQEA.pathNames | Export pathway names from QEA analysis
GetQEATable | QEA table
GetRCommandHistory | Export R Command History
GetRFConf.Table | Classification performance table for random forest analysis
GetRFConfMat | Random Forest Confusion Matrix
GetRFOOB | Random Forest OOB
GetRFSigMat | Random Forest Significance matrix
GetROC.coords | Return ROC corodinates with confidence intervals
GetROCLassoFreq | Get p-values from lasso
GetROCTtestP | Get p-values for ROC
GetSampleSizeLadder | Retrieve sample size ladder
GetSelectedDataNames | Retrieve data names
GetSelectedDataNumber | Retrieve selected data numbers
GetSigTable | Create Latex table
GetSigTable.Anova | Sig Table for Anova
GetSigTable.Aov2 | Sig table for AOV2
GetSigTable.ASCA | Table of features well modelled by ASCA
GetSigTable.Corr | Sig table for Correlation Analysis
GetSigTable.EBAM | Sig table for EBAM
GetSigTable.FC | Sig Table for Fold-Change Analysis
GetSigTable.MB | Sig table for MB analysis
GetSigTable.RF | Sig table for random forest analysis
GetSigTable.SAM | Sig table for SAM
GetSigTable.SVM | Sig table for SVM
GetSigTable.TT | Sig Table for T-test Analysis
GetSigTable.Volcano | Sig table for Volcano Analysis
GetSOMClusterMembers | SOM analysis
GetSSPTable | Replace the last column of the ssp.mat with the final selection from users
GetSuggestedSAMDelta | For SAM analysis
GetSVMSigMat | Recursive Support Vector Machine (R-SVM) Significance Measure
GetTopInx | Volcano indices
GetTrainTestSplitMat | Make random partitions
GetTtestRes | Retrieve T-test p-values
GetTTSigMat | T-test matrix
GetUnivReport | Utility method to perform the univariate analysis automatically
GetVariableLabel | Determine variable label for plotting
GetVennGeneNames | Get Venn names
GetXYCluster | Determine row/column number for plotting
GroupPeakList | Group peak list

## -- H --

heckbert | Heckbert algorithm
HMDBID2KEGGID | Given a vector of HMDBIDs, return a vector of KEGG IDs
HMDBID2Name | Given a vector of HMDBIDs, return a vector of HMDB compound names

## -- I --

ImportRawMSData | Import raw MS data
ImputeVar | Data processing: Replace missing variables
InitDataObjects | Constructs a dataSet object for storing data
InitPowerAnal | Function for power analysis
InitStatAnalMode | Introduction for statistical analysis module report Initialize Statistical Analysis Report
InitTimeSeriesAnal | Create report of analyses (Met Pathway)
iPCA.Anal | Perform PCA analysis, prepare file for interactive liveGraphics3D
isEmptyMatrix | Sig table matrix is empty
IsSmallSmplSize | Check if the sample size is small
IsSpectraProcessingOK | Check if the spectra processing is ok

## -- K --

KEGGID2HMDBID | Given a vector of KEGGIDs, return a vector of HMDB ID
KEGGID2Name | Given a vector containing KEGGIDs, returns a vector of KEGG compound names
KEGGPATHID2SMPDBIDs | Given a vector containing KEGG pathway IDs, return a vector containing SMPDB IDs (only for hsa)
Kmeans.Anal | K-means analysis
kwtest | Kruskal-Wallis

## -- L --

LoadKEGGKO_lib | Utility function for PerformKOEnrichAnalysis_KO01100
LoadKEGGLib | Load KEGG library
LoadMsetLib | Load metabolite set library
LoadSmpLib | Load pathway library
LogNorm | Column-wise Normalization
LSD.test | Calculate Fisher's Least Significant Difference (LSD)

## -- M --

make_cpdlist | Utility function to create compound lists for permutation analysis
map | sPLS-DA Map
MapCmpd2KEGGNodes | Utility function for PrepareQueryJson
MapKO2KEGGEdges | Utility function for PrepareQueryJson
Match.Pattern | Match pattern for correlation analysis
MergeDatasets | Utility function for PrepareQueryJson
MergeDuplicates | Merge duplicated columns or rows by their mean
MetaboliteMappingExact | Mapping from different metabolite IDs
MSspec.fillPeaks | Function to fill in missing peaks
MSspec.rtCorrection | Retention time correction for LC/GC-MS spectra
multi.stat | Get multiple category statistics

## -- N --

Normalization | Normalization

## -- O --

OPLSR.Anal | Perform OPLS-DA

## -- P --

parseFisher | Return only the signicant comparison names
parseTukey | Return only the signicant comparison names
PCA.Anal | Perform PCA analysis
PCA.Flip | Rotate PCA analysis
PCA.GENES | Obtain principal components into a matrix that has more variables than individuals
Perform.ASCA | Perform ASCA
Perform.ASCA.permute | Perform ASCA model validation by permutation
Perform.Permut | Perform permutation tests only for ROC Tester
Perform.permutation | Permutation
Perform.UnivROC | Perform Classical Univariate ROC
PerformAdductMapping | Read Adduct List
PerformApproxMatch | Perform approximate compound matches
PerformBatchCorrection | Set up two matrixes
PerformCurrencyMapping | Map currency metabolites to KEGG & BioCyc
PerformCV.explore | Perform Monte-Carlo Cross Validation (MCCV)
PerformCV.test | Perform MCCV for manually selected features
PerformDetailMatch | Perform detailed name match
PerformEachDEAnal | Performs differential expression analysis on individual data
PerformGeneAnnotation | Perform gene annotation
PerformGSEA | New main function to perform fast pre-ranked mummichog
PerformIndNormalization | Perform normalization for individually-uploaded datasets for meta-analysis
PerformIntegCmpdMapping | Perform compound mapping for integrative analysis methods
PerformIntegGeneMapping | Perform integrated gene mapping
PerformIntegPathwayAnalysis | Perform integrative pathway analysis
PerformKOEnrichAnalysis_KO01100 | Performs KO enrichment analysis based on the KO01100 map
PerformKOEnrichAnalysis_List | Utility function for PerformKOEnrichAnalysis_KO01100
PerformLimmaDE | Perform differential expression analysis using Limma for individually-uploaded data.
PerformMapping | Utility function for PrepareQueryJson geneIDs is text one string, need to make to vector
performMB | Timecourse analysis
PerformMetaMerge | Meta-Analysis Method: Direct merging of datasets
PerformMultiMatch | Perform multiple name matches
PerformMummichog | Main function to perform mummichog
PerformPeakAnnotation | Perform peak annotation This function performs peak annotation on the xset object created using the PerformPeakPicking function.
PerformPeakProfiling | Perform peak annotation This function performs feature extraction of user's raw MS data using the rawData object created using the InspectRawMSData function.
PerformPowerProfiling | Perform power profiling
PerformPvalCombination | Meta-Analysis Method: Combining p-values
PerformVoteCounting | Meta-Analysis Method: Vote Counting
Plot.Permutation | Plot results of permutation tests
PlotAccuracy | Plot classification performance using different features for Multi-Biomarker
PlotANOVA | Plot ANOVA
PlotANOVA2 | Plot Venn diagram of ANOVA results
PlotASCA.Permutation | Plot ASCA permutation
PlotAscaImpVar | Plot the important variables for each factor
PlotASCAModel | Plot score plots of each ASCA model for component 1 against time
PlotCmpdSummary | Plot compound summary change to use dataSet$proc instead of dataSet$orig in case of too many NAs
PlotCmpdView | Plot Compound View
PlotConcRange | Plot the compound concentration data compared to the reference concentration range
PlotCorr | Pattern hunter, correlation plot
PlotCorrHeatMap | Pattern hunter, corr heatmap
PlotDetailROC | Plot detailed ROC
PlotEBAM.A0 | For EBAM analysis
PlotEBAM.Cmpd | Plot EBAM
PlotEIC | Plot EIC This functionn creates an extracted ion chromatogram (EIC) for a specific m/z and retention time. This is used for quality-control of raw m/s data.
PlotEnrichNet.Overview | Barplot height is enrichment fold change
PlotFC | Plot fold change
PlotHCTree | Plot Dendrogram
PlotHeatMap | Create Heat Map Plot
PlotHeatMap2 | Plot heatmap visualization for time-series data
PlotImpVar | Plot PLS important variables,
PlotImpVars | Plot selected compounds by their percentage frequency
PlotInmexGraph | Plot an igraph object and return the node information (position and labels)
PlotInmexPath | Plot integrated methods pathway analysis
PlotIntegPaths | PlotIntegPaths
PlotInteraction | Plot ASCA interaction plots
PlotKEGGPath | Plot metabolome pathway
PlotKmeans | Plot K-means analysis
PlotLoadingCmpd | Plot loading compounds
PlotMBTimeProfile | Plot MB Time Profile
PlotMetaVenn | Meta-Analysis: Plot Venn Diagram
PlotMetpaPath | Plot KEGG pathway
PlotModelScree | Plot scree plots for each model in ASCA
PlotMS.RT | Plot rentention time corrected spectra
PlotMSEA.Overview | Plot MSEA overview
PlotNormSummary | Two plot summary plot: Feature View of before and after normalization
PlotOPLS.MDL | Plot OPLS
PlotOPLS.Permutation | Perform OPLS-DA permutation
PlotOPLS.Splot | S-plot for OPLS-DA
PlotOPLS2DScore | Create OPLS-DA score plot
PlotORA | Plot over-representation analysis (ORA)
PlotPathSummary | Plot a scatterplot (circle) overview of the matched pathways
PlotPCA.overview | Scatter plot colored by different batches
PlotPCA2DScore | Create 2D PCA score plot
PlotPCA3DScore | Create 3D PCA score plot
PlotPCA3DScoreImg | Create 3D PCA score plot
PlotPCABiplot | Create PCA Biplot, set xpd = T to plot outside margin
PlotPCALoading | Plot PCA loadings and also set up the matrix for display
PlotPCAPairSummary | Plot PCA pair summary, format image in png, tiff, pdf, ps, svg
PlotPCAScree | Plot PCA scree plot
PlotPLS.Classification | Plot PLS-DA classification performance using different components
PlotPLS.Imp | Plot PLS important features
PlotPLS.Permutation | Plot PLS-DA classification performance using different components, permutation
PlotPLS2DScore | Plot PLS score plot
PlotPLS3DScore | Plot PLS 3D score plot
PlotPLS3DScoreImg | Plot PLS 3D score plot
PlotPLSLoading | Plot PLS loading plot, also set the loading matrix for display
PlotPLSPairSummary | Plot PLS pairwise summary
PlotPowerProfile | Plot power profile
PlotPowerStat | Plot power statistics
PlotProbView | Plot a summary view of the classification result
plotProfile | Plot the variable across time points (x)
PlotQEA.MetSet | View individual compounds related to a given metabolite set
PlotQEA.Overview | Plot QEA overview
PlotRF.Classify | Plot Random Forest
PlotRF.Outlier | Plot Random Forest outliers
PlotRF.VIP | Plot Random Forest variable importance
PlotROC | Plot ROC
PlotROC.LRmodel | Plot ROC for the logistic regression model
PlotROCTest | Plot ROC for the ROC Curve Based Model Creation and Evaluation module
PlotRSVM.Classification | Recursive Support Vector Machine (R-SVM) plot
PlotRSVM.Cmpd | Recursive Support Vector Machine (R-SVM) plot of important variables
PlotSAM.Cmpd | Plot SAM
PlotSAM.FDR | Plot SAM Delta Plot
PlotSampleNormSummary | Two plot summary plot: Sample View of before and after normalization
PlotSelectedFeature | Create a box-plot of a feature's expression pattern across the different datasets
PlotSigVar | Supporting function for plotting important variables for each factor
PlotSOM | SOM Plot
PlotSPLS2DScore | Score Plot SPLS-DA
PlotSPLS3DScore | 3D SPLS-DA score plot
PlotSPLS3DScoreImg | Plot sPLS-DA 3D score plot
PlotSPLSDA.Classification | Create SPLS-DA classification plot
PlotSPLSLoading | Create SPLS-DA loading plot
PlotSPLSPairSummary | Plot SPLS-DA
PlotSubHeatMap | Create Sub Heat Map Plot
PlotTestAccuracy | Plot classification performance using different features for Biomarker Tester
PlotTT | Plot t-test
PlotVolcano | Create volcano plot
PLSDA.CV | PLS-DA classification and feature selection
PLSDA.Permut | Perform PLS-DA permutation
PLSR.Anal | PLS analysis using oscorespls (Orthogonal scores algorithm) so that VIP can be calculated note: the VIP is calculated only after PLSDA-CV is performed to determine the best # of comp. used for VIP
Predict.class | Get predicted class probability
PrepareIntegData | Prepare integrated data
PrepareNetworkData | Prepare data for network exploration
PreparePDFReport | Create report of analyses
PreparePermResult | Prepare report for permutation tests
PreparePrenormData | Prepare data for normalization
PrepareQueryJson | Prepare user's query for mapping KEGG Global Metabolic Network
PrepareROCData | Prepare data for ROC analysis
PrepareROCDetails | ROC with CI for AUC
PrepareVennData | Prepare data for Venn diagram

## -- R --

RankFeatures | Rank features based on different importance measures
Read.BatchCSVdata | Data I/O for batch effect checking
Read.MSspec | Read LC/GC-MS spectra (.netCDF, .mzXML, mzData)
Read.PeakList | Read peak list files
Read.PeakListData | Constructor to read uploaded user files into the mummichog object
Read.TextData | Constructor to read uploaded CSV or TXT files into the dataSet object
ReadIndData | Read in individual data
ReadPairFile | Read paired peak or spectra files
RecordRCommand | Record R Commands
rectUnique | Perform utilities for peak grouping
RegisterData | Register data in R
RemoveCmpd | Remove selected compounds
RemoveData | Remove data object, the current dataSet will be the last one by default
RemoveDuplicates | Given a data with duplicates, remove duplicates
RemoveFile | Remove file
RemoveFolder | Remove folder
RemoveGene | Remove selected genes
RemoveMissingPercent | Data processing: remove variables with missing values
ReplaceMin | Replace missing or zero values
RerenderMetPAGraph | Redraw current graph for zooming or clipping then return a value
RF.Anal | Perform Random Forest Analysis
ROCPredSamplesTable | Create a table of newly classified samples
RSVM | R-SVM core code
RSVM.Anal | Recursive Support Vector Machine (R-SVM)

## -- S --

SAM.Anal | Perform Signifiance Analysis of Microarrays (SAM) analysis
SanityCheckData | Sanity Check Data
SanityCheckIndData | Sanity check of individual datasets for meta-analysis
SanityCheckMummichogData | Sanity Check Data
SaveTransformedData | Save the processed data with class names
SearchByCompound | Search for compound from all member compounds of metabolite set
SearchByName | Given a metabolite set name, search its index
SearchMsetLibraries | Search metabolite set libraries
SearchNetDB | Perform mapping of user's data to interaction network
SelectMultiData | Select one or more datasets for meta-analysis
SetAnalysisMode | Set biomarker analysis mode
SetAnnotationParam | Set annotation parameters
SetCachexiaSetUsed | Set the cachexia set used
SetCandidate | Set matched name based on user selection from all potential hits
SetCurrentGroups | To choose from two groups
SetCurrentMsetLib | Set current user selected metset library for search
SetCustomData | Set custom data
SetDesignType | For two factor time series only
SetEBAMSigMat | For EBAM analysis
SetKEGG.PathLib | Set KEGG pathway library
SetMetabolomeFilter | Set metabolome filter
SetOrganism | Set organism for further analysis
SetPeakList.GroupValues | Set peak list group values
SetPeakParam | Set parameters for peak picking using XCMS and CAMERA
SetSAMSigMat | Set Signifiance Analysis of Microarrays (SAM) analysis matrix
SetSMPDB.PathLib | Set SMPDB pathway library
Setup.AdductData | Save adduct names for mapping
Setup.BiofluidType | Save biofluid type for SSP
Setup.ConcData | Save concentration data
Setup.HMDBReferenceMetabolome | Read user uploaded metabolome as a list of HMDB compound names
Setup.KEGGReferenceMetabolome | Read user uploaded metabolome as a list of KEGG pathway ids
Setup.MapData | Save compound name for mapping
Setup.UserMsetLibData | Read user upload metabolite set library file
SetupKEGGLinks | Only works for human (hsa.rda) data
SetupMSdataMatrix | Create a MS spectra data matrix of peak values for each group
SetupSMPDBLinks | Only works for human (hsa.rda) data
SOM.Anal | SOM analysis
sparse.mint.block_iteration | Perform Sparse Generalized Canonical Correlation (sgccak)
splsda | Perform sPLS-DA
SPLSR.Anal | Perform SPLS-DA
SumNorm | Row-wise Normalization

## -- T --

template.match | Pattern hunter
Ttests.Anal | Perform t-test analysis

## -- U --

UnzipUploadedFile | Unzip .zip files
UpdateIntegPathwayAnalysis | Update integrative pathway analysis for new input list
UpdateMummichogParameters | Update the mSetObj with user-selected parameters for MS Peaks to Pathways.
UpdateOPLS.Splot | Update OPLS loadings
UpdatePCA.Loading | Update PCA loadings
UpdatePLS.Loading | Update PLS loadings
usr2png | Perform utilities for MetPa

## -- V --

Volcano.Anal | Perform Volcano Analysis

## -- X --

XSet2MSet | Converts xset object from XCMS to mSet object for MetaboAnalyst

## -- misc --

.read.metaboanalyst.lib | Read RDS files from the internet
.readDataTable | Read data table