Files in xia-lab/MetaboAnalystR
An R Package for Comprehensive Analysis of Metabolomics Data

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
MetaboAnalystR.Rproj
NAMESPACE
R/all_generic_utils.R R/batch_effect_utils.R R/biomarker_utils.R R/depends_refs.R R/dose_response_deanal.R R/dose_response_general.R R/dose_response_graphs.R R/dose_response_utils.R R/duplicates_estimates.R R/enrich_graphics.R R/enrich_integ.R R/enrich_kegg.R R/enrich_mset.R R/enrich_name_match.R R/enrich_path_graphics.R R/enrich_path_stats.R R/enrich_stats.R R/gene_fun_utils.R R/general_anot_utils.R R/general_data_utils.R R/general_lib_utils.R R/general_misc_utils.R R/general_norm_utils.R R/general_proc_utils.R R/generic_c_utils.R R/meta_data_utils.R R/meta_methods.R R/meta_pathway.R R/mgwas_data.R R/mgwas_misc.R R/mgwas_mr.R R/multifac_asca_heatmap2.R R/multifac_covariate.R R/multifac_mb.R R/multifac_metadata.R R/multifac_pca_anova2.R R/networks_enrich.R R/networks_view.R R/others_lipomics.R R/peaks_ms2fun.R R/peaks_to_function.R R/plotly_utils.R R/power_utils.R R/rpackage_config.R R/spectra_processing.R R/stats_chemometrics.R R/stats_classification.R R/stats_clustering.R R/stats_correlations.R R/stats_opls.R R/stats_peaks.R R/stats_plot3d.R R/stats_sigfeatures.R R/stats_spls.R R/stats_univariates.R R/sweave_report_biomarker.R R/sweave_report_enrichment.R R/sweave_report_integmex.R R/sweave_report_meta_analysis.R R/sweave_report_metamummi.R R/sweave_report_mummichog.R R/sweave_report_network.R R/sweave_report_pathway.R R/sweave_report_power.R R/sweave_report_raw_spectra.R R/sweave_report_stats.R R/sweave_report_time.R R/sweave_reporter.R R/tandem_ms.R R/util_api.R R/util_approx.R R/util_batch.R R/util_compatibility.R R/util_fgsea.R R/util_heatmap.R R/util_lipid.R R/util_listheatmap.R R/util_lsd.R R/util_metabolon.R R/util_missing.R R/util_multifac_mb_1d.R R/util_multifac_mb_2d.R R/util_multifac_mb_manova.R R/util_mztab.R R/util_nmdr.R R/util_peaks.R R/util_plot3d.R R/util_psea.R R/util_savedata.R R/util_scatter3d.R R/util_sspa.R R/util_univreport.R R/util_venndiagram.R R/util_volcano.R README.md
inst/CITATION
inst/docs/MetaboAnalystR_3.0.0_manual.pdf
inst/docs/MetaboAnalystRlogo.png
inst/docs/cran-comments.md
inst/docs/log_v3.0.png
inst/lists/ions.csv
inst/lists/neutraladdition.csv
inst/lists/neutralloss.csv
inst/rules/extended_adducts_neg.csv
inst/rules/extended_adducts_pos.csv
inst/rules/primary_adducts_neg.csv
inst/rules/primary_adducts_pos.csv
man/ANOVA.Anal.Rd man/ANOVA2.Anal.Rd man/ASCAfun.res.Rd man/ASCAfun1.Rd man/ASCAfun2.Rd man/AddErrMsg.Rd man/CalculateFeatureRanking.Rd man/CalculateGlobalTestScore.Rd man/CalculateHyperScore.Rd man/CalculateImpVarCutoff.Rd man/CalculateOraScore.Rd man/CalculatePairwiseDiff.Rd man/CalculateQeaScore.Rd man/CalculateSSP.Rd man/CentroidCheck.Rd man/CheckMetaDataConsistency.Rd man/CleanData.Rd man/CleanDataMatrix.Rd man/CleanNumber.Rd man/ClearStrings.Rd man/ComputeAverageCurve.Rd man/ComputeHighLow.Rd man/ContainMissing.Rd man/Convert2AnalObject.Rd man/Convert2Mummichog.Rd man/Convert2MummichogMetaPath.Rd man/CovariateScatter.Anal.Rd man/CreateANOVAdoc.Rd man/CreateAOV2doc.Rd man/CreateASCAdoc.Rd man/CreateAnalNullMsg.Rd man/CreateBiomarkerInputDoc.Rd man/CreateBiomarkerIntr.Rd man/CreateBiomarkerOverview.Rd man/CreateBiomarkerRatioOverview.Rd man/CreateBiomarkerRnwReport.Rd man/CreateCorAnalysis.Rd man/CreateCorHeatmap.Rd man/CreateCorrDoc.Rd man/CreateCovAdj.Rd man/CreateEBAMdoc.Rd man/CreateEnrichAnalDoc.Rd man/CreateEnrichInputDoc.Rd man/CreateEnrichIntr.Rd man/CreateEnrichORAdoc.Rd man/CreateEnrichOverview.Rd man/CreateEnrichProcessDoc.Rd man/CreateEnrichQEAdoc.Rd man/CreateEnrichRnwReport.Rd man/CreateEnrichSSPdoc.Rd man/CreateFooter.Rd man/CreateGSEAAnalTable.Rd man/CreateGraph.Rd man/CreateHCdoc.Rd man/CreateIntegMatchingTable.Rd man/CreateIntegPathwayAnalysisRnwReport.Rd man/CreateIntegratedPathwayAnalInputDoc.Rd man/CreateIntegratedPathwayAnalIntr.Rd man/CreateIntegratedPathwayDoc.Rd man/CreateIntegratedPathwayGeneMapTable.Rd man/CreateIntegratedPathwayNameMapTable.Rd man/CreateIntegratedPathwayResultsTable.Rd man/CreateKMdoc.Rd man/CreateLadder.Rd man/CreateMBdoc.Rd man/CreateMappingResultTable.Rd man/CreateMetaAnalTable.Rd man/CreateMetaAnalysisDEdoc.Rd man/CreateMetaAnalysisInputDoc.Rd man/CreateMetaAnalysisIntr.Rd man/CreateMetaAnalysisNORMdoc.Rd man/CreateMetaAnalysisOutput.Rd man/CreateMetaAnalysisOverview.Rd man/CreateMetaAnalysisRnwReport.Rd man/CreateMetaMummichogInputDoc.Rd man/CreateMetaMummichogIntro.Rd man/CreateMetaMummichogResults.Rd man/CreateMetaOverview.Rd man/CreateMetaPathRnwReport.Rd man/CreateMetaTable.Rd man/CreateModelBiomarkersDoc.Rd man/CreateMultiBiomarkersDoc.Rd man/CreateMummichogAnalTable.Rd man/CreateMummichogAnalysisDoc.Rd man/CreateMummichogInputDoc.Rd man/CreateMummichogIntro.Rd man/CreateMummichogLibs.Rd man/CreateMummichogMetaAnalPathTable.Rd man/CreateMummichogMetaAnalReport.Rd man/CreateMummichogOverview.Rd man/CreateMummichogRnwReport.Rd man/CreateNORMdoc.Rd man/CreateNetworkExplorerDoc.Rd man/CreateNetworkExplorerInputDoc.Rd man/CreateNetworkExplorerIntr.Rd man/CreateNetworkExplorerOverview.Rd man/CreateNetworkExplorerRnwReport.Rd man/CreateNetworkGeneMapTable.Rd man/CreateNetworkNameMapTable.Rd man/CreateOPLSDAdoc.Rd man/CreatePCAdoc.Rd man/CreatePLSdoc.Rd man/CreatePathAnalDoc.Rd man/CreatePathInputDoc.Rd man/CreatePathIntr.Rd man/CreatePathProcessDoc.Rd man/CreatePathResultDoc.Rd man/CreatePathRnwReport.Rd man/CreatePowerAnalDoc.Rd man/CreatePowerInputDoc.Rd man/CreatePowerIntr.Rd man/CreatePowerOverview.Rd man/CreatePowerParametersDoc.Rd man/CreatePowerRnwReport.Rd man/CreateRFdoc.Rd man/CreateRHistAppendix.Rd man/CreateROCLabelsTable.Rd man/CreateRandomForest.Rd man/CreateRatioTable.Rd man/CreateRawAnalysisRnwReport.Rd man/CreateSAMdoc.Rd man/CreateSOMdoc.Rd man/CreateSPLSDAdoc.Rd man/CreateSVMdoc.Rd man/CreateSemiTransColors.Rd man/CreateStatIOdoc.Rd man/CreateStatIntr.Rd man/CreateStatRnwReport.Rd man/CreateSummaryTable.Rd man/CreateTimeSeriesAnalNullMsg.Rd man/CreateTimeSeriesIOdoc.Rd man/CreateTimeSeriesRnwReport.Rd man/CreateUNIVdoc.Rd man/CreateUnivROCTable.Rd man/CreateUnivarBiomarkersDoc.Rd man/CreateVennMetaTable.Rd man/CreateiPCAdoc.Rd man/CrossReferencing.Rd man/EBAM.Init.Rd man/FC.Anal.Rd man/FeatureCorrelation.Rd man/FilterVariable.Rd man/FisherLSD.Rd man/GeneratePeakList.Rd man/Get.ConcRef.Rd man/Get.Leverage.Rd man/Get.VIP.Rd man/Get.asca.tss.Rd man/Get.bwss.Rd man/Get.pAUC.Rd man/Get.pred.Rd man/Get.rpart.summary.Rd man/GetAbundanceLabel.Rd man/GetAccuracyInfo.Rd man/GetAllDataNames.Rd man/GetAllKMClusterMembers.Rd man/GetAllSOMClusterMembers.Rd man/GetCIs.Rd man/GetCMD.Rd man/GetCandidateList.Rd man/GetCircleInfo.Rd man/GetCompoundDetails.Rd man/GetConvertFullPath.Rd man/GetExtendRange.Rd man/GetFC.Rd man/GetFeatureNumbers.Rd man/GetFinalNameMap.Rd man/GetFisherPvalue.Rd man/GetGroupNames.Rd man/GetHTMLMetSet.Rd man/GetHTMLPathSet.Rd man/GetImpFeatureMat.Rd man/GetKEGGNodeInfo.Rd man/GetKMClusterMembers.Rd man/GetLassoFreqs.Rd man/GetLimmaResTable.Rd man/GetMapTable.Rd man/GetMaxPCAComp.Rd man/GetMeanROC.Rd man/GetMetSetName.Rd man/GetMetaResultMatrix.Rd man/GetMsetLibCheckMsg.Rd man/GetMsetNames.Rd man/GetMummichogPathSetDetails.Rd man/GetNMDRStudy.Rd man/GetNetworkGeneMappingResultTable.Rd man/GetNewSampleNames.Rd man/GetORA.pathNames.Rd man/GetORA.smpdbIDs.Rd man/GetORATable.Rd man/GetQEA.keggIDs.Rd man/GetQEA.pathNames.Rd man/GetQEATable.Rd man/GetRCommandHistory.Rd man/GetRFConf.Table.Rd man/GetRFConfMat.Rd man/GetRFOOB.Rd man/GetRFSigMat.Rd man/GetROC.coords.Rd man/GetROCLassoFreq.Rd man/GetROCTtestP.Rd man/GetSOMClusterMembers.Rd man/GetSSPTable.Rd man/GetSVMSigMat.Rd man/GetSampleSizeLadder.Rd man/GetSigTable.ASCA.Rd man/GetSigTable.Anova.Rd man/GetSigTable.Aov2.Rd man/GetSigTable.Corr.Rd man/GetSigTable.Dose.Rd man/GetSigTable.EBAM.Rd man/GetSigTable.FC.Rd man/GetSigTable.MB.Rd man/GetSigTable.RF.Rd man/GetSigTable.Rd man/GetSigTable.SAM.Rd man/GetSigTable.SVM.Rd man/GetSigTable.TT.Rd man/GetSigTable.Volcano.Rd man/GetSuggestedSAMDelta.Rd man/GetTTSigMat.Rd man/GetTopInx.Rd man/GetTrainTestSplitMat.Rd man/GetTtestRes.Rd man/GetUnivReport.Rd man/GetVariableLabel.Rd man/GetXYCluster.Rd man/GroupPeakList.Rd man/HMDBID2KEGGID.Rd man/HMDBID2Name.Rd man/ImputeMissingVar.Rd man/InitDataObjects.Rd man/InitMSObjects.Rd man/InitPowerAnal.Rd man/InitStatAnalMode.Rd man/InitTimeSeriesAnal.Rd man/InitializaPlan.Rd man/IsSmallSmplSize.Rd man/KEGGID2HMDBID.Rd man/KEGGID2Name.Rd man/KEGGPATHID2SMPDBIDs.Rd man/Kmeans.Anal.Rd man/ListNMDRStudies.Rd man/LoadKEGGKO_lib.Rd man/LogNorm.Rd man/MapCmpd2KEGGNodes.Rd man/MapKO2KEGGEdges.Rd man/Match.Pattern.Rd man/MergeDatasets.Rd man/MergeDuplicates.Rd man/MetaPathNormalization.Rd man/MetaboAnalystR.Rd man/MetaboliteMappingExact.Rd man/Normalization.Rd man/OPLSDA.Permut.Rd man/OPLSR.Anal.Rd man/PCA.Anal.Rd man/PCA.Flip.Rd man/PCA.GENES.Rd man/PLSDA.CV.Rd man/PLSDA.Permut.Rd man/PLSR.Anal.Rd man/Perform.ASCA.Rd man/Perform.ASCA.permute.Rd man/Perform.Permut.Rd man/Perform.UnivROC.Rd man/Perform.permutation.Rd man/PerformAdductMapping.Rd man/PerformApproxMatch.Rd man/PerformBatchCorrection.Rd man/PerformCV.explore.Rd man/PerformCV.test.Rd man/PerformCmpdMapping.Rd man/PerformCurrencyMapping.Rd man/PerformDataInspect.Rd man/PerformDataTrimming.Rd man/PerformDetailMatch.Rd man/PerformEachDEAnal.Rd man/PerformGeneMapping.Rd man/PerformIndNormalization.Rd man/PerformIntegPathwayAnalysis.Rd man/PerformKOEnrichAnalysis_KO01100.Rd man/PerformKOEnrichAnalysis_List.Rd man/PerformLimmaDE.Rd man/PerformMS1ResultsFormatting.Rd man/PerformMS2ResultsFormatting.Rd man/PerformMapping_ko01100.Rd man/PerformMetaMerge.Rd man/PerformMetaPSEA.Rd man/PerformMirrorPlotting.Rd man/PerformMirrorPlottingWeb.Rd man/PerformMultiMatch.Rd man/PerformPSEA.Rd man/PerformParamsOptimization.Rd man/PerformPeakProfiling.Rd man/PerformPowerProfiling.Rd man/PerformPvalCombination.Rd man/PerformROIExtraction.Rd man/PerformSignalDriftCorrection.Rd man/PerformVoteCounting.Rd man/Plot.Permutation.Rd man/Plot.sampletrend.Rd man/PlotANOVA.Rd man/PlotANOVA2.Rd man/PlotASCA.Permutation.Rd man/PlotASCAModel.Rd man/PlotAccuracy.Rd man/PlotAscaImpVar.Rd man/PlotClustPCA.Rd man/PlotCmpdSummary.Rd man/PlotCmpdView.Rd man/PlotConcRange.Rd man/PlotCorr.Rd man/PlotCorrHeatMap.Rd man/PlotDetailROC.Rd man/PlotEBAM.Cmpd.Rd man/PlotEnrichDotPlot.Rd man/PlotEnrichNet.Overview.Rd man/PlotEnrichPieChart.Rd man/PlotFC.Rd man/PlotHCTree.Rd man/PlotHeatMap.Rd man/PlotHeatMap2.Rd man/PlotImpBiomarkers.Rd man/PlotImpVar.Rd man/PlotImpVarMeta.Rd man/PlotInmexGraph.Rd man/PlotInmexPath.Rd man/PlotInteraction.Rd man/PlotKEGGPath.Rd man/PlotKmeans.Rd man/PlotMBTimeProfile.Rd man/PlotMSEA.Overview.Rd man/PlotMetaCorrHeatmap.Rd man/PlotMetaHeatmap.Rd man/PlotMetpaPath.Rd man/PlotModelScree.Rd man/PlotMultiFacCmpdSummary.Rd man/PlotNormSummary.Rd man/PlotOPLS.Imp.Rd man/PlotOPLS.MDL.Rd man/PlotOPLS.Permutation.Rd man/PlotOPLS.Splot.Rd man/PlotOPLS2DScore.Rd man/PlotORA.Rd man/PlotPCA.overview.Rd man/PlotPCA2DScore.Rd man/PlotPCA3DLoading.Rd man/PlotPCA3DScore.Rd man/PlotPCA3DScoreImg.Rd man/PlotPCABiplot.Rd man/PlotPCALoading.Rd man/PlotPCAPairSummary.Rd man/PlotPCAScree.Rd man/PlotPLS.Classification.Rd man/PlotPLS.Imp.Rd man/PlotPLS.Permutation.Rd man/PlotPLS2DScore.Rd man/PlotPLS3DLoading.Rd man/PlotPLS3DScore.Rd man/PlotPLS3DScoreImg.Rd man/PlotPLSLoading.Rd man/PlotPLSPairSummary.Rd man/PlotPSEAIntegPaths.Rd man/PlotPathSummary.Rd man/PlotPathwayMetaAnalysis.Rd man/PlotPeaks2Paths.Rd man/PlotPowerProfile.Rd man/PlotPowerStat.Rd man/PlotProbView.Rd man/PlotProbViewTest.Rd man/PlotQEA.MetSet.Rd man/PlotQEA.Overview.Rd man/PlotRF.Classify.Rd man/PlotRF.ClassifyMeta.Rd man/PlotRF.Outlier.Rd man/PlotRF.VIP.Rd man/PlotRF.VIPMeta.Rd man/PlotROC.LRmodel.Rd man/PlotROC.Rd man/PlotROCTest.Rd man/PlotRSVM.Classification.Rd man/PlotRSVM.Cmpd.Rd man/PlotRocUnivBoxPlot.Rd man/PlotSAM.Cmpd.Rd man/PlotSAM.FDR.Rd man/PlotSOM.Rd man/PlotSPLS2DScore.Rd man/PlotSPLS3DLoading.Rd man/PlotSPLS3DScore.Rd man/PlotSPLS3DScoreImg.Rd man/PlotSPLSDA.Classification.Rd man/PlotSPLSLoading.Rd man/PlotSPLSPairSummary.Rd man/PlotSampleNormSummary.Rd man/PlotSelectedFeature.Rd man/PlotSigVar.Rd man/PlotStaticCorrHeatMap.Rd man/PlotStaticHeatMap.Rd man/PlotStaticHeatMap2.Rd man/PlotStaticMetaHeatmap.Rd man/PlotSubHeatMap.Rd man/PlotTT.Rd man/PlotTestAccuracy.Rd man/PlotVolcano.Rd man/PlotXIC.Rd man/Predict.class.Rd man/PrepareIntegData.Rd man/PrepareKeggQueryJson.Rd man/PrepareMetaPath.Rd man/PrepareNetworkData.Rd man/PreparePDFReport.Rd man/PreparePeakTable4PSEA.Rd man/PreparePermResult.Rd man/PreparePrenormData.Rd man/PrepareROCData.Rd man/PrepareROCDetails.Rd man/PrepareUpsetData.Rd man/RF.Anal.Rd man/RF.AnalMeta.Rd man/ROCPredSamplesTable.Rd man/RSVM.Anal.Rd man/RSVM.Rd man/RankFeatures.Rd man/Read.BatchDataBC.Rd man/Read.BatchDataTB.Rd man/Read.PeakList.Rd man/Read.PeakListData.Rd man/Read.SignalDriftData.Rd man/Read.TextData.Rd man/Read.TextDataTs.Rd man/Read.mzTab.Rd man/ReadIndData.Rd man/ReadMetaData.Rd man/ReadMetaPathTable.Rd man/ReadMetaPathTableMix.Rd man/ReadPairFile.Rd man/RecordRCommand.Rd man/RegisterData.Rd man/RemoveCmpd.Rd man/RemoveData.Rd man/RemoveDuplicates.Rd man/RemoveFile.Rd man/RemoveFolder.Rd man/RemoveGene.Rd man/RemoveMissingPercent.Rd man/ReplaceMin.Rd man/RerenderMetPAGraph.Rd man/SAM.Anal.Rd man/SOM.Anal.Rd man/SPLSR.Anal.Rd man/SaintyCheckMSPfile.Rd man/SanityCheckData.Rd man/SanityCheckIndData.Rd man/SanityCheckMeta.Rd man/SanityCheckMetaPathTable.Rd man/SanityCheckMummichogData.Rd man/SaveTransformedData.Rd man/SearchByCompound.Rd man/SearchByName.Rd man/SearchMsetLibraries.Rd man/SearchNetDB.Rd man/SelectMultiData.Rd man/SetAnalysisMode.Rd man/SetCachexiaSetUsed.Rd man/SetCandidate.Rd man/SetCurrentGroups.Rd man/SetCurrentMsetLib.Rd man/SetCustomData.Rd man/SetDataTypeOfMeta.Rd man/SetDesignType.Rd man/SetKEGG.PathLib.Rd man/SetMetabolomeFilter.Rd man/SetMummichogPval.Rd man/SetMummichogPvalFromPercent.Rd man/SetOrganism.Rd man/SetPeakEnrichMethod.Rd man/SetPeakFormat.Rd man/SetPeakList.GroupValues.Rd man/SetPeakParam.Rd man/SetRTincluded.Rd man/SetSMPDB.PathLib.Rd man/Setup.AdductData.Rd man/Setup.BiofluidType.Rd man/Setup.ConcData.Rd man/Setup.HMDBReferenceMetabolome.Rd man/Setup.KEGGReferenceMetabolome.Rd man/Setup.MapData.Rd man/Setup.UserMsetLibData.Rd man/SetupKEGGLinks.Rd man/SetupSMPDBLinks.Rd man/SumNorm.Rd man/Ttests.Anal.Rd man/UnzipUploadedFile.Rd man/UpdateData.Rd man/UpdateEC_Rules.Rd man/UpdateGraphSettings.Rd man/UpdateInstrumentParameters.Rd man/UpdateIntegPathwayAnalysis.Rd man/UpdateOPLS.Splot.Rd man/UpdatePCA.Loading.Rd man/UpdatePLS.Loading.Rd man/Volcano.Anal.Rd man/XSet2MSet.Rd man/analyze.lipids.Rd man/aof.Rd man/aov.1wayrep.Rd man/aov.2way.Rd man/aov.mixed.Rd man/calculateConcISO.Rd man/computeConc.Rd man/createCVset.Rd man/descendMin.Rd man/doCompoundMapping.Rd man/doGeneIDMapping.Rd man/doKEGG2NameMapping.Rd man/doKOFiltering.Rd man/doLogisticRegMdl.Rd man/dot-do.CVTest.LRmodel.Rd man/dot-get.my.lib.Rd man/dot-readDataTable.Rd man/findEqualGreaterM.Rd man/getDataFromTextArea.Rd man/heckbert.Rd man/iPCA.Anal.Rd man/isEmptyMatrix.Rd man/kwtest.Rd man/make_cpdlist.Rd man/make_ecpdlist.Rd man/map.Rd man/melt.Rd man/multi.stat.Rd man/my.lsd.test.Rd man/my.parse.peaklist.Rd man/parseFisher.Rd man/parseTukey.Rd man/performMB.Rd man/performMS2searchBatch.Rd man/performMS2searchSingle.Rd man/plotMSfeature.Rd man/plotMirror.Rd man/plotProfile.Rd man/plotSingleTIC.Rd man/plot_dist.Rd man/processMSMSupload.Rd man/rectUnique.Rd man/savePeakListMetaData.Rd man/setInclusionDataSets.Rd man/setMS2DBOpt.Rd man/sparse.mint.block_iteration.Rd man/splsda.Rd man/template.match.Rd man/usr2png.Rd
src/Exports.cpp
src/Makevars
src/Makevars.win
src/c/Internal_utils_batch.c
src/c/Internal_utils_batch.h
src/c/common.h
src/c/fastmatch.c
src/c/mzROI.c
src/c/nncgc.c
src/c/util.c
src/c/util.h
src/c/xcms_binners.c
src/c/xcms_binners.h
src/cpp/melt.cpp
src/fortran/decorana.f
tests/testthat.R tests/testthat/test-basic.R tests/testthat/test-metaboanalystr-analytical.R tests/testthat/test-metaboanalystr-pathway-enrichment.R
xia-lab/MetaboAnalystR documentation built on May 25, 2024, 8:10 p.m.