| AddErrMsg | Adds an error message |
| add_trace | I. Internal Functions from Plotly Package THe functions are... |
| analyze.lipids | Lipid analysis pipeliner |
| ANOVA2.Anal | Perform Two-way ANOVA |
| ANOVA.Anal | Perform ANOVA analysis |
| aof | ANOVA |
| aov.between | Perform Two-way ANOVA |
| aov.repeated | Perform Two-way ANOVA |
| aov.within | Perform Two-way ANOVA |
| ASCAfun1 | Function to perform ASCA |
| ASCAfun2 | Function to perform ASCA |
| ASCAfun.res | Function to perform ASCA |
| calcCV | Calculatre CV method |
| calcGaussianS | Calculatre Gaussian Peak Ratio method |
| calcPPS2 | Calculate PPS method |
| calcRCS_GSValues | Calculatre RCS and GS method |
| calculateConcISO | Calculate Concentration ISO |
| CalculateFeatureRanking | Calculates feature importance |
| CalculateGlobalTestScore | Quantitative enrichment analysis with globaltest |
| calculateGPRT | Alignment Method |
| CalculateHyperScore | Over-representation analysis using hypergeometric tests |
| CalculateImpVarCutoff | Calculate the Important Variable Cutoff |
| CalculateOraScore | Calculate ORA score |
| CalculatePairwiseDiff | Calculate Pairwise Differences |
| calculatePPKs | Peak picking Method |
| CalculateQeaScore | Calculate quantitative enrichment score |
| calculateSet_doe | Cluster of Peak Picking and Alignment |
| CalculateSSP | Single sample profiling to compare with |
| CheckMetaDataConsistency | Check if data are ready for meta-analysis |
| C_imodwt_r | Internal C fucntion - C_imodwt_r |
| 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 |
| C_modwt_r | Internal C fucntion - C_modwt_r |
| Compound_function_mzlist | Makes adducts |
| 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... |
| CreateAnalNullMsg | Create null message for analysis Creates a message for the... |
| 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... |
| CreateGSEAAnalTable | Create Mummichog report of analyses |
| 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 |
| CreateLibFromKEGG | Creates cpd.tree |
| 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) |
| CreateMetaTable | Create MetaAnalysis table of results |
| CreateModelBiomarkersDoc | Create biomarker analysis report: ROC Curve Based Model... |
| CreateMultiBiomarkersDoc | Create biomarker analysis report: Multivariate Biomarker... |
| 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 |
| 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 |
| creatPeakTable | creatPeakTable |
| CrossReferencing | Various functions for mapping b/w names & database... |
| CVTest.LRmodel | Calculate ROC performance with CV |
| Densitygrouping_slave | Densitygrouping_slave |
| doCompoundMapping | Perform compound mapping |
| doGeneIDMapping | Convert different gene IDs into entrez IDs for downstream... |
| doKEGG2NameMapping | Perform KEGG to compound name mapping |
| doKOFiltering | Utility function |
| dot-compute.mummichog.fgsea | Internal function for calculating GSEA, no RT |
| dot-compute.mummichog.RT.fgsea | Internal function for calculating GSEA, with RT |
| dot-emptyscan.remove | Function for 'Empty scan' removal |
| dot-init.Permutations | Internal function to perform PSEA, no retention time |
| dot-init.RT.Permutations | Internal function to perform PSEA, with RT |
| dot-readDataTable | Read data table |
| dot-read.metaboanalyst.lib | Read RDS files from the internet |
| EBAM.Init | For EBAM analysis |
| ExperimentsCluster_doe | Experiment Functions of DoE |
| ExtractMS2data | Extract MS2 Data |
| 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 |
| fillpathways | Fill in the pathways |
| FilterVariable | Methods for non-specific filtering of variables |
| FisherLSD | Fisher for ANOVA |
| FormatPeakList | Format Peak List |
| genLogisticRegMdl | Develop a Logistic Regression Model with all of the combined... |
| 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 |
| Get.asca.tss | Function for ASCA permutation |
| Get.bwss | Compute within group and between group sum of squares... |
| 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 |
| Get.ConcRef | Get the concentration reference |
| 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... |
| 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 |
| Get.Leverage | Fast leverage calculation for permutation purpose |
| 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... |
| 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 |
| 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 |
| GetORA.pathNames | Export pathway names from ORA analysis |
| GetORA.smpdbIDs | Only for human pathways (SMPDB) |
| GetORATable | Get ORA table |
| Get.pAUC | Calculate partial area under ROC curve |
| Get.pred | Get predicted class probability |
| GetQEA.keggIDs | Only for human pathways (KEGG) |
| GetQEA.pathNames | Export pathway names from QEA analysis |
| GetQEATable | QEA table |
| GetRCommandHistory | Export R Command History |
| GetRFConfMat | Random Forest Confusion Matrix |
| GetRFConf.Table | Classification performance table for random forest analysis |
| 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 |
| Get.rpart.summary | Get the text description of a recursive partitioning (rpart)... |
| 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... |
| 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... |
| GetVariableLabel | Determine variable label for plotting |
| GetVennGeneNames | Get Venn names |
| Get.VIP | Calculate variable importance of projection (VIP) score for... |
| GetXYCluster | Determine row/column number for plotting |
| GroupPeakList | Group peak list |
| 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... |
| ImportRawMSData | Import raw MS data |
| ImportRawMSDataList | 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... |
| InitTimeSeriesAnal | Create report of analyses (Met Pathway) |
| iPCA.Anal | Perform PCA analysis, prepare file for interactive... |
| isEmptyMatrix | Sig table matrix is empty |
| IsSmallSmplSize | Check if the sample size is small |
| IsSpectraProcessingOK | Check if the spectra processing is ok |
| KEGGID2HMDBID | Given a vector of KEGGIDs, return a vector of HMDB ID |
| KEGGID2Name | Given a vector containing KEGGIDs, returns a vector of KEGG... |
| KEGGPATHID2SMPDBIDs | Given a vector containing KEGG pathway IDs, return a vector... |
| Kmeans.Anal | K-means analysis |
| kwtest | Kruskal-Wallis |
| LoadKEGGKO_lib | Utility function for PerformKOEnrichAnalysis_KO01100 |
| LoadKEGGLib | Load KEGG library |
| LoadSmpLib | Load pathway library |
| LogNorm | Column-wise Normalization |
| LSD.test | Calculate Fisher's Least Significant Difference (LSD) |
| make_cpdlib | Gets names and exact mass of all cpds (cpd.lib) |
| make_cpdlist | Utility function to create compound lists for permutation... |
| make_ecpdlist | Utility function to create compound lists for permutation... |
| 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 |
| MetaboAnalystR | MetaboAnalystR: A package for computating the notorious bar... |
| MetaboliteMappingExact | Mapping from different metabolite IDs |
| mSet2xcmsSet | mSet2xcmsSet |
| MSspec.fillPeaks | Function to fill in missing peaks |
| MSspec.rtCorrection | Retention time correction for LC/GC-MS spectra |
| multi.stat | Get multiple category statistics |
| mz.trim_random | Data trimming Method Based on Random MS |
| mz.trim_specific | Data trimming Method Based on Specific MS |
| Noise_evaluate | Noise_evaluation based on Kernal density model |
| Normalization | Normalization |
| OPLSDA.Permut | Perform OPLS-DA permutation |
| OPLSR.Anal | Perform OPLS-DA |
| optimize.xcms.doe | Overall Funtion for DoE |
| optimizxcms.doe.peakpicking | Core Optimization Function of DoE |
| 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... |
| PeakPicking_centWave_slave | PeakPicking_centWave_slave |
| PeakPicking_core | Calculate PPS method |
| PeakPicking_MatchedFilter_slave | PeakPicking_MatchedFilter_slave |
| PeakPicking_prep | Data Preparation for ChromPeaking Finding |
| PerformAdductMapping | Read Adduct List |
| PerformApproxMatch | Perform approximate compound matches |
| Perform.ASCA | Perform ASCA |
| Perform.ASCA.permute | Perform ASCA model validation by permutation |
| PerformBatchCorrection | Batch Effect Correction |
| PerformCurrencyMapping | Map currency metabolites to KEGG & BioCyc |
| PerformCV.explore | Perform Monte-Carlo Cross Validation (MCCV) |
| PerformCV.test | Perform MCCV for manually selected features |
| PerformDataInspect | Data inspectation |
| PerformDataTrimming | Perform raw MS data trimming |
| PerformDetailMatch | Perform detailed name match |
| PerformEachDEAnal | Performs differential expression analysis on individual data |
| PerformIndNormalization | Perform normalization for individually-uploaded datasets for... |
| 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... |
| PerformMapping | Utility function for PrepareQueryJson geneIDs is text one... |
| performMB | Timecourse analysis |
| PerformMetaMerge | Meta-Analysis Method: Direct merging of datasets |
| PerformMSDataOutput | Function MS Generation |
| PerformMultiMatch | Perform multiple name matches |
| PerformParamsOptimization | Perform Parameters Optimization |
| PerformPeakAlignment | PerformPeakAlignment |
| PerformPeakAnnotation | Perform peak annotation |
| PerformPeakFiling | PerformPeakFiling |
| PerformPeakGrouping | PerformPeakGrouping |
| PerformPeakPicking | PerformPeakPicking |
| PerformPeakProfiling | Perform peak profiling This function performs feature... |
| Perform.Permut | Perform permutation tests only for ROC Tester |
| Perform.permutation | Permutation |
| PerformPowerProfiling | Perform power profiling |
| PerformPSEA | Function to perform peak set enrichment analysis |
| PerformPvalCombination | Meta-Analysis Method: Combining p-values |
| Perform.UnivROC | Perform Classical Univariate ROC |
| PerformVoteCounting | Meta-Analysis Method: Vote Counting |
| PlotAccuracy | Plot classification performance using different features for... |
| PlotANOVA | Plot ANOVA |
| PlotANOVA2 | Plot Venn diagram of ANOVA results |
| PlotAscaImpVar | Plot the important variables for each factor |
| PlotASCAModel | Plot score plots of each ASCA model for component 1 against... |
| PlotASCA.Permutation | Plot ASCA permutation |
| PlotBoxPlot | Plot a boxplot view of a selected compound |
| PlotCmpdSummary | Plot compound summary change to use dataSet$proc instead of... |
| PlotCmpdView | Plot Compound View |
| PlotConcRange | Plot the compound concentration data compared to the... |
| PlotCorr | Pattern hunter, correlation plot |
| PlotCorrHeatMap | Pattern hunter, corr heatmap |
| PlotDetailROC | Plot detailed ROC |
| PlotEBAM.Cmpd | Plot EBAM |
| PlotEIC | Plot EIC |
| 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... |
| 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 |
| PlotMS2Spectra | Plot selected M2 spectra for an m/z feature |
| plot.MS_3D | Function for 3D ms plotting |
| PlotMSEA.Overview | Plot MSEA overview |
| PlotMSPeaksPerm | Plot MS Peaks to Paths mummichog permutation p-values |
| PlotMS.RT | Plot rentention time corrected spectra |
| PlotNormSummary | Two plot summary plot: Feature View of before and after... |
| PlotOPLS2DScore | Create OPLS-DA score plot |
| PlotOPLS.MDL | Plot OPLS |
| PlotOPLS.Permutation | Plot OPLS-DA permutation |
| PlotOPLS.Splot | S-plot for OPLS-DA |
| PlotORA | Plot over-representation analysis (ORA) |
| PlotPathSummary | Plot a scatterplot (circle) overview of the matched pathways |
| PlotPathwayMZHits | Plot m/z hits in a pathway |
| 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 |
| PlotPCA.overview | Scatter plot colored by different batches |
| PlotPCAPairSummary | Plot PCA pair summary, format image in png, tiff, pdf, ps,... |
| PlotPCAScree | Plot PCA scree plot |
| PlotPeaks2Paths | PlotPeaks2Paths |
| Plot.Permutation | Plot results of permutation tests |
| PlotPLS2DScore | Plot PLS score plot |
| PlotPLS3DScore | Plot PLS 3D score plot |
| PlotPLS3DScoreImg | Plot PLS 3D score plot |
| PlotPLS.Classification | Plot PLS-DA classification performance using different... |
| PlotPLS.Imp | Plot PLS important features |
| PlotPLSLoading | Plot PLS loading plot, also set the loading matrix for... |
| PlotPLSPairSummary | Plot PLS pairwise summary |
| PlotPLS.Permutation | Plot PLS-DA classification performance using different... |
| 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... |
| PlotRSVM.Classification | Recursive Support Vector Machine (R-SVM) plot |
| PlotRSVM.Cmpd | Recursive Support Vector Machine (R-SVM) plot of important... |
| PlotSAM.Cmpd | Plot SAM |
| PlotSAM.FDR | Plot SAM Delta Plot |
| PlotSampleNormSummary | Two plot summary plot: Sample View of before and after... |
| Plot.sampletrend | Sample Trend Scatter |
| PlotSelectedFeature | Create a box-plot of a feature's expression pattern across... |
| PlotSigVar | Supporting function for plotting important variables for each... |
| 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... |
| 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)... |
| 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... |
| PrepareROCData | Prepare data for ROC analysis |
| PrepareROCDetails | ROC with CI for AUC |
| PrepareVennData | Prepare data for Venn diagram |
| RankFeatures | Rank features based on different importance measures |
| rda2list | Utility function Make list of KEGG rda files |
| Read.BatchCSVdata | Data I/O for batch effect checking |
| ReadIndData | Read in individual data |
| Read.MSspec | Read LC/GC-MS spectra (.netCDF, .mzXML, mzData) |
| ReadPairFile | Read paired peak or spectra files |
| Read.PeakList | Read peak list files |
| Read.PeakListData | Constructor to read uploaded user files into the mummichog... |
| Read.TextData | Constructor to read uploaded CSV or TXT files into the... |
| RecordRCommand | Record R Commands |
| RegisterData | Register data in R |
| RemoveCmpd | Remove selected compounds |
| RemoveData | Remove data object, the current dataSet will be the last one... |
| 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... |
| resultIncreased_doe | Identify whether results improved or not |
| 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) |
| RT.Adjust_Slave | RT.Adjust_Slave |
| rt.trim_random | Data trimming Method Based on Random RT |
| rt.trim_specific | Data trimming Method Based on Specific RT |
| 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... |
| 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... |
| SetClass | Set class information for MS data |
| 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 |
| SetKEGG.PathLib | Set KEGG pathway library |
| SetMetabolomeFilter | Set metabolome filter |
| 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... |
| SetPeakFormat | Set the peak format for the mummichog analysis |
| SetPeakList.GroupValues | Set peak list group values |
| SetPeakParam | Set parameters for peak profiling and parameters optimization |
| SetPlotParam | Set generic Plotting Parameters |
| 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... |
| SetupKEGGLinks | Only works for human (hsa.rda) data |
| Setup.KEGGReferenceMetabolome | Read user uploaded metabolome as a list of KEGG pathway ids |
| Setup.MapData | Save compound name for mapping |
| SetupMSdataMatrix | Create a MS spectra data matrix of peak values for each group |
| SetupSMPDBLinks | Only works for human (hsa.rda) data |
| Setup.UserMsetLibData | Read user upload metabolite set library file |
| SlaveCluster_doe | Core Peak Picking Slave Cluster |
| SOM.Anal | SOM analysis |
| sparse.mint.block_iteration | Perform Sparse Generalized Canonical Correlation (sgccak) |
| splsda | Perform sPLS-DA |
| SPLSR.Anal | Perform SPLS-DA |
| ssm_trim | Standards Simulation Method |
| Statistic_doe | Analyze DoE Result |
| SumNorm | Row-wise Normalization |
| template.match | Pattern hunter |
| Ttests.Anal | Perform t-test analysis |
| UnzipUploadedFile | Unzip .zip files |
| UpdateData | Update data for filtering |
| UpdateEC_Rules | Update the mSetObj with user-selected parameters for MS Peaks... |
| UpdateGraphSettings | Update graph settings |
| UpdateInstrumentParameters | Update the mSetObj with user-selected parameters for MS Peaks... |
| UpdateIntegPathwayAnalysis | Update integrative pathway analysis for new input list |
| UpdateOPLS.Splot | Update OPLS loadings |
| UpdatePCA.Loading | Update PCA loadings |
| UpdatePLS.Loading | Update PLS loadings |
| updateRawSpectraParam | updateRawSpectraParam |
| usr2png | Perform utilities for MetPa |
| Volcano.Anal | Perform Volcano Analysis |
| XSet2MSet | Converts xset object from XCMS to mSet object for... |
