An R Package for Comprehensive Analysis of Metabolomics Data
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Documentation for package ‘MetaboAnalystR’ version 4.0.0
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.1wayrep | Perform Two-way ANOVA |
| aov.2way | Perform Two-way ANOVA |
| aov.mixed | Perform Two-way ANOVA |
| ASCAfun.res | Function to perform ASCA |
| ASCAfun1 | Function to perform ASCA Adapted from online R script with performance tuning |
| 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 | Calculate the Important Variable Cutoff |
| CalculateOraScore | Calculate ORA score |
| CalculatePairwiseDiff | Calculate Pairwise Differences |
| CalculateQeaScore | Calculate quantitative enrichment score |
| CalculateSSP | Single sample profiling to compare with |
| CentroidCheck | CentroidCheck |
| CheckMetaDataConsistency | Check if data are ready for meta-analysis |
| CleanData | Perform data cleaning |
| CleanDataMatrix | Clean the data matrix |
| CleanNumber | Replace infinite numbers |
| ClearStrings | Remove spaces |
| ComputeAverageCurve | Compute average ROC curve |
| computeConc | Lipid analysis |
| ComputeHighLow | Compute the 95 percent interval for threshold ROC |
| ContainMissing | Check for missing data |
| Convert2AnalObject | Convert2AnalObject This function is used to convert mSet object from raw spectra processing for the following analysis. |
| Convert2Mummichog | Convert mSetObj to proper format for MS Peaks to Pathways module |
| Convert2MummichogMetaPath | Convert mSetObj to proper format for MS Peaks to Pathways module |
| CovariateScatter.Anal | CovariateScatter.Anal |
| 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) |
| CreateCorAnalysis | Create report of analyses |
| CreateCorHeatmap | Create report of analyses |
| CreateCorrDoc | Create report of analyses |
| CreateCovAdj | 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 |
| CreateGSEAAnalTable | Create Mummichog report of analyses |
| CreateHCdoc | Create report of analyses |
| CreateIntegMatchingTable | CreateIntegMatchingTable |
| 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 |
| CreateMetaAnalTable | Create Mummichog 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) |
| CreateMetaMummichogInputDoc | Create analysis report: Functional Meta-Analysis Data Input |
| CreateMetaMummichogIntro | Create analysis report: Functional Meta-Analysis Introduction |
| CreateMetaMummichogResults | Create analysis report: Functional Meta-Analysis Results |
| CreateMetaOverview | Create report of analyses |
| CreateMetaPathRnwReport | Create report of analyses (Biomarker) |
| 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 |
| CreateMummichogLibs | Create Mummichog Libraries from KEGG |
| CreateMummichogMetaAnalPathTable | Create analysis report: Functional Meta-Analysis Results Table |
| CreateMummichogMetaAnalReport | Create analysis report: Functional Meta-Analysis |
| 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) |
| CreateRandomForest | Create report of analyses |
| CreateRatioTable | Create report of analyses |
| CreateRawAnalysisRnwReport | Create report for raw spectra module |
| 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 |
-- D --
| descendMin | Perform utilities for peak grouping |
| doCompoundMapping | Perform compound mapping |
| doGeneIDMapping | Convert different gene IDs into entrez IDs for downstream analysis |
| doKEGG2NameMapping | Perform KEGG to compound name mapping |
| doKOFiltering | Utility function |
| doLogisticRegMdl | Develop a Logistic Regression Model with all of the combined k-fold CV subsets |
-- E --
| EBAM.Init | For EBAM analysis |
-- F --
| FC.Anal | Fold change analysis, unpaired |
| FeatureCorrelation | Pattern hunter |
| FilterVariable | Methods for non-specific filtering of variables |
| findEqualGreaterM | Perform utilities for peak grouping |
| FisherLSD | Fisher for ANOVA |
-- G --
| GeneratePeakList | GeneratePeakList |
| 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 |
| GetCompoundDetails | Function to get adduct details from a specified compound |
| 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 |
| GetGroupNames | Get all group names |
| 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 |
| GetMetSetName | Given a metset inx, give its name |
| GetMsetLibCheckMsg | Get the library check messages |
| GetMsetNames | Return the selected metset library to java for display |
| GetMummichogPathSetDetails | Function to get compound details from a specified pathway |
| GetNetworkGeneMappingResultTable | Exports Gene-Mapping result into a table |
| GetNewSampleNames | Obtain sample names and their class labels |
| GetNMDRStudy | Function to retrieve dataset from the Metabolomics Workbench. |
| 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 |
| 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.Dose | Sig Table for Anova |
| 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 |
| 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 --
| ImputeMissingVar | Data processing: Replace missing variables |
| InitDataObjects | Constructs a dataSet object for storing data |
| InitializaPlan | InitializePlan |
| InitMSObjects | InitMSObjects |
| 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 |
-- 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 --
| ListNMDRStudies | Function to retrieve all available datasets from the Metabolomics Workbench. |
| LoadKEGGKO_lib | Utility function for PerformKOEnrichAnalysis_KO01100 |
| LogNorm | Column-wise Normalization |
-- M --
| make_cpdlist | Utility function to create compound lists for permutation analysis |
| make_ecpdlist | Utility function to create compound lists for permutation analysis |
| map | sPLS-DA Map |
| MapCmpd2KEGGNodes | Utility function for PrepareKeggQueryJson |
| MapKO2KEGGEdges | Utility function for PrepareKeggQueryJson |
| Match.Pattern | Match pattern for correlation analysis |
| melt | melt Convert an object into a molten data frame. This function is from reshape2 package. |
| MergeDatasets | Utility function for PrepareKeggQueryJson |
| MergeDuplicates | Merge duplicated columns or rows by their mean |
| MetaboAnalystR | MetaboAnalystR: A package for computating the notorious bar statistic. |
| MetaboliteMappingExact | Mapping from different metabolite IDs |
| MetaPathNormalization | MetaPathNormalization |
| multi.stat | Get multiple category statistics |
| my.lsd.test | Calculate Fisher's Least Significant Difference (LSD) |
| my.parse.peaklist | my.parse.peaklist |
-- N --
| Normalization | Normalization |
-- O --
| OPLSDA.Permut | Perform OPLS-DA permutation |
| 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 | PerformAdductMapping |
| PerformApproxMatch | Perform approximate compound matches |
| PerformBatchCorrection | Batch Effect Correction |
| PerformCmpdMapping | Perform compound mapping for integrative analysis methods |
| PerformCurrencyMapping | Map currency metabolites to KEGG & BioCyc |
| PerformCV.explore | Perform Monte-Carlo Cross Validation (MCCV) |
| PerformCV.test | Perform MCCV for manually selected features |
| PerformDataInspect | PerformDataInspect |
| PerformDataTrimming | Perform ROI Extraction from raw MS data (PerformDataTrimming) |
| PerformDetailMatch | Perform detailed name match |
| PerformEachDEAnal | Performs differential expression analysis on individual data |
| PerformGeneMapping | Perform integrated gene mapping |
| PerformIndNormalization | Perform normalization for individually-uploaded datasets for meta-analysis |
| 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_ko01100 | Utility function for PrepareKeggQueryJson geneIDs is text one string, need to make to vector |
| performMB | Timecourse analysis |
| PerformMetaMerge | Meta-Analysis Method: Direct merging of datasets |
| PerformMetaPSEA | PerformMetaPSEA Function to perform peak set enrichment meta-analysis at either the empirical compound, compound level or pathway level. |
| PerformMirrorPlotting | PerformMirrorPlotting |
| PerformMirrorPlottingWeb | PerformMirrorPlottingWeb |
| PerformMS1ResultsFormatting | PerformMS1ResultsFormatting This function is used to format the results from other tools into the generic format of MetaboAnalystR Currently,we are supporting the compatibility for four commonly used open-source tools: MS-DIAL, MZmine, Asari and XCMS online The first parameter file_path should be a valid file of the result. User need to specify the type in the 2nd argument, type. This argument can be msdial, mzmine, asari and xcms Please note, if your original data does not contain meta information, you need to manually add them in the generated "metaboanalyst_input.csv" file The formatted file is 'sample in columns'. |
| PerformMS2ResultsFormatting | PerformMS2ResultsFormatting This function is used to format the results from other tools into the generic format of MetaboAnalystR for functional analysis Currently,we are supporting the compatibility for four commonly used open-source tools: MS-FINDER, and SIRIUS The first parameter file_path should be a valid file of the result. User need to specify the type in the 2nd argument, type. This argument can be msfinder, or sirius The 3rd column |
| performMS2searchBatch | performMS2searchBatch |
| performMS2searchSingle | performMS2searchSingle |
| PerformMultiMatch | Perform multiple name matches |
| PerformParamsOptimization | Perform Parameters Optimization |
| PerformPeakProfiling | PerformPeakProfiling |
| PerformPowerProfiling | Perform power profiling |
| PerformPSEA | Function to perform peak set enrichment analysis |
| PerformPvalCombination | Meta-Analysis Method: Combining p-values |
| PerformROIExtraction | Perform ROI Extraction from raw MS data (PerformDataTrimming) |
| PerformSignalDriftCorrection | Signal Drift Correction |
| PerformVoteCounting | Meta-Analysis Method: Vote Counting |
| Plot.Permutation | Plot results of permutation tests |
| Plot.sampletrend | Sample Trend Scatter |
| 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 |
| PlotClustPCA | Plot K-means summary PCA plot |
| 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.Cmpd | Plot EBAM |
| PlotEnrichDotPlot | Plot MSEA Dot Plot |
| PlotEnrichNet.Overview | PlotEnrichNet.Overview |
| PlotEnrichPieChart | Create a pie chart for compound classes |
| PlotFC | Plot fold change |
| PlotHCTree | Plot Dendrogram |
| PlotHeatMap | Create Heat Map Plot |
| PlotHeatMap2 | Plot heatmap visualization for time-series data |
| PlotImpBiomarkers | Plot selected compounds by their percentage frequency |
| PlotImpVar | Plot PLS important variables, |
| PlotImpVarMeta | Plot PLS important variables, |
| PlotInmexGraph | Plot an igraph object and return the node information (position and labels) |
| PlotInmexPath | Plot integrated methods pathway analysis |
| PlotInteraction | Plot ASCA interaction plots |
| PlotKEGGPath | Plot metabolome pathway |
| PlotKmeans | Plot K-means analysis |
| PlotMBTimeProfile | Plot MB Time Profile |
| PlotMetaCorrHeatmap | Generate correlation heatmap for metadata |
| PlotMetaHeatmap | Generate heatmaps for metadata table |
| PlotMetpaPath | Plot KEGG pathway |
| plotMirror | plotMirror |
| PlotModelScree | Plot scree plots for each model in ASCA |
| PlotMSEA.Overview | Plot MSEA overview |
| plotMSfeature | plotMSfeature |
| PlotMultiFacCmpdSummary | Plot compound summary for multi-linear regression tool |
| PlotNormSummary | Two plot summary plot: Feature View of before and after normalization |
| PlotOPLS.Imp | PlotOPLS.Imp OPLS VIP plotting function |
| PlotOPLS.MDL | Plot OPLS |
| PlotOPLS.Permutation | Plot 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 |
| PlotPathwayMetaAnalysis | PlotPathwayMetaAnalysis |
| PlotPCA.overview | Scatter plot colored by different batches |
| PlotPCA2DScore | Create 2D PCA score plot |
| PlotPCA3DLoading | PlotPCA3DLoading |
| 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 |
| PlotPeaks2Paths | PlotPeaks2Paths |
| 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 |
| PlotPLS3DLoading | PlotPLS3DLoading |
| 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 |
| PlotProbViewTest | Plot a summary view of the classification result of tester prediction |
| plotProfile | Plot the variable across time points (x) |
| PlotPSEAIntegPaths | PlotPSEAIntegPaths |
| PlotQEA.MetSet | View individual compounds related to a given metabolite set |
| PlotQEA.Overview | Plot QEA overview |
| PlotRF.Classify | Plot Random Forest |
| PlotRF.ClassifyMeta | Plot Random Forest |
| PlotRF.Outlier | Plot Random Forest outliers |
| PlotRF.VIP | Plot Random Forest variable importance |
| PlotRF.VIPMeta | 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 |
| PlotRocUnivBoxPlot | Plot a boxplot view of a selected compound |
| 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 |
| plotSingleTIC | plotSingleTIC |
| PlotSOM | SOM Plot |
| PlotSPLS2DScore | Score Plot SPLS-DA |
| PlotSPLS3DLoading | PlotSPLS3DLoading |
| 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 |
| PlotStaticCorrHeatMap | Create high resolution static HeatMap for download only |
| PlotStaticHeatMap | Create high resolution static HeatMap for download only |
| PlotStaticHeatMap2 | Create high resolution static HeatMap for download only |
| PlotStaticMetaHeatmap | Create high resolution static HeatMap for download only |
| PlotSubHeatMap | Create Sub Heat Map Plot |
| PlotTestAccuracy | Plot classification performance using different features for Biomarker Tester |
| PlotTT | Plot t-test |
| PlotVolcano | Create volcano plot |
| PlotXIC | PlotXIC |
| plot_dist | Batch Distance Plotting |
| 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 |
| PrepareKeggQueryJson | Prepare user's query for mapping KEGG Global Metabolic Network |
| PrepareMetaPath | PrepareMetaPath |
| PrepareNetworkData | Prepare data for network exploration |
| PreparePDFReport | Create report of analyses |
| PreparePeakTable4PSEA | PreparePeakTable4PSEA |
| PreparePermResult | Prepare report for permutation tests |
| PreparePrenormData | Prepare data for normalization |
| PrepareROCData | Prepare data for ROC analysis |
| PrepareROCDetails | ROC with CI for AUC |
| PrepareUpsetData | Prepare data for Upset diagram |
| processMSMSupload | processMSMSupload |
-- R --
| RankFeatures | Rank features based on different importance measures |
| Read.BatchDataBC | Data I/O for batch effect checking |
| Read.BatchDataTB | Data I/O for batch effect checking |
| Read.mzTab | Read an mzTab tab separated file from the passed in file. Adapted from: https://github.com/lifs-tools/rmzTab-m/blob/master/R/MzTabReader.r |
| Read.PeakList | Read peak list files |
| Read.PeakListData | Constructor to read uploaded user files into the mummichog object |
| Read.SignalDriftData | Data I/O for signal drift checking |
| Read.TextData | Read.TextData Constructor to read uploaded CSV or TXT files into the dataSet object |
| Read.TextDataTs | Read.TextDataTs |
| ReadIndData | Read in individual data |
| ReadMetaData | ReadMetaData |
| ReadMetaPathTable | ReadMetaPathTable |
| ReadMetaPathTableMix | ReadMetaPathTableMix |
| 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 |
| RF.AnalMeta | 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 --
| SaintyCheckMSPfile | SaintyCheckMSPfile |
| SAM.Anal | Perform Signifiance Analysis of Microarrays (SAM) analysis |
| SanityCheckData | Sanity Check Data |
| SanityCheckIndData | Sanity check of individual datasets for meta-analysis |
| SanityCheckMeta | SanityCheckMeta#' |
| SanityCheckMetaPathTable | SanityCheckMetaPathTable |
| SanityCheckMummichogData | Sanity Check Data |
| savePeakListMetaData | Function to save each mSetObj as a RDS file to be used later in PerformMetaPSEA. Should be called after SetPeakEnrichMethod/SetMummichogPval |
| 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 |
| 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 |
| SetDataTypeOfMeta | SetDataTypeOfMeta |
| SetDesignType | For two factor time series only |
| setInclusionDataSets | setInclusionDataSets#' |
| SetKEGG.PathLib | Set KEGG pathway library |
| SetMetabolomeFilter | Set metabolome filter |
| setMS2DBOpt | setMS2DBOpt |
| SetMummichogPval | Set the cutoff for mummichog analysis |
| SetMummichogPvalFromPercent | Set the cutoff for mummichog analysis |
| SetOrganism | Set organism for further analysis |
| SetPeakEnrichMethod | Set the peak enrichment method for the MS Peaks to Paths module |
| SetPeakFormat | Set the peak format for the mummichog analysis |
| SetPeakList.GroupValues | Set peak list group values |
| SetPeakParam | SetPeakParam |
| SetRTincluded | SetRTincluded |
| 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 |
| 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 |
| UpdateData | Update data for filtering |
| UpdateEC_Rules | Update the mSetObj with user-selected parameters for MS Peaks to Pathways. |
| UpdateGraphSettings | Update graph settings |
| UpdateInstrumentParameters | Update the mSetObj with user-selected parameters for MS Peaks to Pathways. |
| UpdateIntegPathwayAnalysis | Update integrative pathway analysis for new input list |
| 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 --
| .do.CVTest.LRmodel | Calculate ROC performance with CV An internal function called by PerformCV.test |
| .get.my.lib | Read RDS files from the internet |
| .readDataTable | Read data table |