An R Package for Comprehensive Analysis of Metabolomics Data


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Documentation for package ‘MetaboAnalystR’ version 2.0.0

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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