{ "_id": "6a10a942acfb0bcc41cbe88d", "Package": "patRoon", "Type": "Package", "Title": "Workflows for Mass-Spectrometry Based Non-Target Analysis", "Version": "3.0.0", "Authors@R": "c(\nperson(\"Rick\", \"Helmus\",\nemail = \"r.helmus@uva.nl\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9401-3133\")\n),\nperson(\"Olaf\", \"Brock\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4727-8459\")\n),\nperson(\"Vittorio\", \"Albergamo\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-5347-1362\")\n),\nperson(\"Andrea\", \"Brunner\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2801-1751\")\n),\nperson(\"Emma\", \"Schymanski\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-6868-8145\")\n),\nperson(\"Bas\", \"van de Velde\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1292-3251\"),\n),\nperson(\"Leon\", \"Saal\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-3522-7729\"),\n))", "Description": "Provides an easy-to-use interface to a mass spectrometry\nbased non-target analysis workflow. Various (open-source) tools\nare combined which provide algorithms for extraction and\ngrouping of features, extraction of MS and MS/MS data,\nautomatic formula and compound annotation and grouping related\nfeatures to components. 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"loadMSLibraryMoNAJSON", "loadMSLibraryMSP", "makeFileHash", "makeHash", "makeHCluster", "makeSet", "merge", "MetFragAdducts", "MSLibrary", "MSPeakLists", "MSPeakListsSet", "MSPeakListsUnset", "newProject", "normInts", "numericIDLevel", "optimizationResult", "optimizedObject", "optimizedParameters", "optimizeFeatureFinding", "optimizeFeatureGrouping", "overlap", "parents", "peakLists", "plot", "plotBPCs", "plotChord", "plotChroms", "plotChroms3D", "plotGraph", "plotHeatMap", "plotInt", "plotMobilograms", "plotScores", "plotSilhouettes", "plotSpectrum", "plotStructure", "plotTICs", "plotUpSet", "plotVenn", "plotVolcano", "predictCheckFeaturesSession", "predictRespFactors", "predictTox", "printPackageOpts", "products", "recalibrarateDAFiles", "records", "replicates", "replicateSubtract", "report", "reportCSV", "reportHTML", "reportPDF", "revertDAAnalyses", "saveCacheData", "scores", "screenInfo", "screenSuspects", "selectIons", "setDAMethod", "setObjects", "sets", "settings", "show", "showDataAnalysis", "spectra", "spectrumSimilarity", "spectrumSimilarityIMS", "toxicities", "TPLogicTransformations", "transformationProducts", "transformationProductsAnnComp", "transformationProductsAnnForm", "transformationProductsFormula", "transformationProductsLogic", "transformationProductsStructure", "treeCut", "treeCutDynamic", "unique", "unset", "updateGroups", "verifyDependencies", "withOpt", "workflowStep", "workflowStepSet" ], "_help": [ { "page": "patRoon-package", "title": "Workflow solutions for mass-spectrometry based non-target analysis.", "topics": [ "patRoon-package", "patRoon" ] }, { "page": "adduct-class", "title": "Generic adduct class", "topics": [ "adduct", "adduct-class", "as.character,adduct-method", "show,adduct-method" ] }, { "page": "adduct-utils", "title": "Adduct utilities", "topics": [ "adduct-utils", "as.adduct", "calculateIonFormula", "calculateNeutralFormula", "GenFormAdducts", "MetFragAdducts" ] }, { "page": "analysis-information", "title": "Properties of sample analyses", "topics": [ "analysis-information", "generateAnalysisInfo", "generateAnalysisInfoFromEnviMass" ] }, { "page": "analysisinfo-dataframe", "title": "AnalysisInfo data.frame methods", "topics": [ "analysisinfo-dataframe", "getBPCs,data.frame-method", "getTICs,data.frame-method", "plotBPCs,data.frame-method", "plotBPCs,data.table-method", "plotTICs,data.frame-method", "plotTICs,data.table-method" ] }, { "page": "assignMobilities_comp", "title": "Assign IMS data to a 'compounds' object.", "topics": [ "assignMobilities,compounds-method", "assignMobilities,compoundsSet-method", "assignMobilities_comp" ] }, { "page": "assignMobilities_feat", "title": "Assign Ion Mobility and CCS values to features", "topics": [ "assignMobilities,featureGroups-method", "assignMobilities,featureGroupsScreening-method", "assignMobilities,featureGroupsScreeningSet-method", "assignMobilities,featureGroupsSet-method", "assignMobilities_feat" ] }, { "page": "assignMobilities_susp", "title": "Assign IMS data to suspects", "topics": [ "assignMobilities,data.frame-method", "assignMobilities,data.table-method", "assignMobilities_susp" ] }, { "page": "bruker-utils", "title": "Bruker DataAnalysis utilities", "topics": [ "addAllDAEICs", "addDAEIC", "bruker-utils", "getDACalibrationError", "recalibrarateDAFiles", "revertDAAnalyses", "setDAMethod", "showDataAnalysis" ] }, { "page": "C3SDBAdducts", "title": "Returns the adducts supported by C3SDB", "topics": [ "C3SDBAdducts" ] }, { "page": "caching", "title": "Utilities for caching of workflow data.", "topics": [ "caching", "clearCache", "loadCacheData", "makeFileHash", "makeHash", "saveCacheData" ] }, { "page": "CCS-Conversion", "title": "Conversion between mobility and CCS", "topics": [ "CCS-Conversion", "convertCCSToMobility", "convertMobilityToCCS" ] }, { "page": "check-GUI", "title": "Interactive GUI utilities to check workflow data", "topics": [ "check-GUI", "checkComponents", "checkComponents,components-method", "checkFeatures", "checkFeatures,featureGroups-method", "getMCTrainData", "importCheckFeaturesSession", "predictCheckFeaturesSession" ] }, { "page": "cluster-params", "title": "Clustering parameters", "topics": [ "cluster-params" ] }, { "page": "components-class", "title": "Component class", "topics": [ "$,components-method", "as.data.table,components-method", "componentInfo", "componentInfo,components-method", "components", "components-class", "componentsCamera", "componentsCamera-class", "componentsCliqueMS", "componentsCliqueMS-class", "componentsFeatures", "componentsFeatures-class", "componentsOpenMS", "componentsOpenMS-class", "componentsRC", "componentsRC-class", "componentsSet", "componentsSet-class", "componentsUnset", "componentsUnset-class", "componentTable", "componentTable,components-method", "consensus,components-method", "consensus,componentsSet-method", "delete,components-method", "delete,componentsSet-method", "expandForIMS", "expandForIMS,components-method", "expandForIMS,componentsCamera-method", "expandForIMS,componentsCliqueMS-method", "expandForIMS,componentsNT-method", "expandForIMS,componentsNTSet-method", "expandForIMS,componentsOpenMS-method", "expandForIMS,componentsRC-method", "expandForIMS,componentsSet-method", "filter,components-method", "filter,componentsSet-method", "findFGroup", "findFGroup,components-method", "groupNames,components-method", "length,components-method", "names,components-method", "plotChroms,components-method", "plotSpectrum,components-method", "show,components-method", "show,componentsFeatures-method", "show,componentsSet-method", "unset,componentsSet-method", "[,components,ANY,ANY,missing-method", "[,componentsSet,ANY,ANY,missing-method", "[[,components,ANY,ANY-method" ] }, { "page": "componentsClust-class", "title": "Base class for components that are based on hierarchical clustered data.", "topics": [ "clusterProperties,componentsClust-method", "clusters,componentsClust-method", "componentsClust", "componentsClust-class", "cutClusters,componentsClust-method", "delete,componentsClust-method", "plot,componentsClust,missing-method", "plotSilhouettes,componentsClust-method", "treeCut,componentsClust-method", "treeCutDynamic,componentsClust-method" ] }, { "page": "componentsIntClust-class", "title": "Components based on clustered intensity profiles.", "topics": [ "componentsIntClust", "componentsIntClust-class", "plotHeatMap", "plotHeatMap,componentsIntClust-method", "plotInt,componentsIntClust-method" ] }, { "page": "componentsNT-class", "title": "Components class for homologous series.", "topics": [ "componentsNT", "componentsNT-class", "componentsNTSet", "componentsNTSet-class", "componentsNTUnset", "componentsNTUnset-class", "plotGraph,componentsNT-method", "plotGraph,componentsNTSet-method", "unset,componentsNTSet-method" ] }, { "page": "componentsSpecClust-class", "title": "Components based on MS/MS similarity.", "topics": [ "componentsSpecClust", "componentsSpecClust-class" ] }, { "page": "componentsTPs-class", "title": "Components based on parent and transformation product (TP) linkage.", "topics": [ "as.data.table,componentsTPs-method", "componentsTPs", "componentsTPs-class", "filter,componentsTPs-method", "plotGraph,componentsTPs-method" ] }, { "page": "compounds-class", "title": "Compound annotations class", "topics": [ "addFormulaScoring", "addFormulaScoring,compounds-method", "addFormulaScoring,compoundsSet-method", "annotatedPeakList,compounds-method", "annotatedPeakList,compoundsSet-method", "compounds", "compounds-class", "compoundsConsensus", "compoundsConsensus-class", "compoundsConsensusSet", "compoundsConsensusSet-class", "compoundsSet", "compoundsSet-class", "compoundsUnset", "compoundsUnset-class", "consensus,compounds-method", "consensus,compoundsSet-method", "defaultExclNormScores,compounds-method", "delete,compoundsSet-method", "delete,compoundsSIRIUS-method", "filter,compounds-method", "filter,compoundsSet-method", "getMCS,compounds-method", "identifiers", "identifiers,compounds-method", "plotScores,compounds-method", "plotSpectrum,compounds-method", "plotSpectrum,compoundsSet-method", "plotStructure,compounds-method", "show,compounds-method", "show,compoundsSet-method", "unset,compoundsConsensusSet-method", "unset,compoundsSet-method", "[,compoundsSet,ANY,missing,missing-method" ] }, { "page": "compounds-cluster", "title": "Hierarchical clustering of compounds", "topics": [ "compounds-cluster", "makeHCluster", "makeHCluster,compounds-method" ] }, { "page": "compoundsCluster-class", "title": "Compounds cluster class", "topics": [ "clusterProperties,compoundsCluster-method", "clusters,compoundsCluster-method", "compoundsCluster", "compoundsCluster-class", "cutClusters,compoundsCluster-method", "getMCS,compoundsCluster-method", "groupNames,compoundsCluster-method", "length,compoundsCluster-method", "lengths,compoundsCluster-method", "plot,compoundsCluster,missing-method", "plotSilhouettes,compoundsCluster-method", "plotStructure,compoundsCluster-method", "show,compoundsCluster-method", "treeCut,compoundsCluster-method", "treeCutDynamic,compoundsCluster-method", "[,compoundsCluster,ANY,missing,missing-method" ] }, { "page": "compoundScorings", "title": "Scorings terms for compound candidates", "topics": [ "compoundScorings" ] }, { "page": "compoundsMF-class", "title": "Compounds list class for MetFrag results.", "topics": [ "compoundsMF", "compoundsMF-class", "settings", "settings,compoundsMF-method" ] }, { "page": "compoundsSIRIUS-class", "title": "Compounds class for SIRIUS results.", "topics": [ "compoundsSIRIUS", "compoundsSIRIUS-class" ] }, { "page": "defaultOpenMSAdducts", "title": "Default adducts for OpenMS componentization", "topics": [ "defaultOpenMSAdducts" ] }, { "page": "EIXParams", "title": "Extracted Ion Chromatogram and Mobilogram parameters", "topics": [ "EIXParams", "getDefEICParams", "getDefEIMParams" ] }, { "page": "feature-filtering", "title": "Filtering of grouped features", "topics": [ "feature-filtering", "filter,featureGroups-method", "filter,featureGroupsSet-method", "replicateSubtract", "replicateSubtract,featureGroups-method" ] }, { "page": "feature-optimization", "title": "Optimization of feature finding and grouping parameters", "topics": [ "feature-optimization", "generateFeatureOptPSet", "generateFGroupsOptPSet", "getDefFeaturesOptParamRanges", "getDefFGroupsOptParamRanges", "optimizeFeatureFinding", "optimizeFeatureGrouping" ] }, { "page": "feature-plotting", "title": "Plotting of grouped features", "topics": [ "feature-plotting", "plot,featureGroups,missing-method", "plotBPCs,featureGroups-method", "plotChord,featureGroups-method", "plotChroms,featureGroups-method", "plotChroms3D,featureGroups-method", "plotChroms3D,featureGroupsSet-method", "plotGraph,featureGroups-method", "plotGraph,featureGroupsSet-method", "plotInt,featureGroups-method", "plotMobilograms", "plotMobilograms,featureGroups-method", "plotTICs,featureGroups-method", "plotUpSet,featureGroups-method", "plotVenn,featureGroups-method", "plotVolcano,featureGroups-method" ] }, { "page": "feature-quality", "title": "Feature quality definitions and utilities", "topics": [ "feature-quality", "featureGroupQualities", "featureQualities", "featureQualityNames" ] }, { "page": "feature-table", "title": "Feature group to table conversion", "topics": [ "as.data.table,featureGroups-method", "as.data.table,featureGroupsScreening-method", "as.data.table,featureGroupsScreeningSet-method", "feature-table" ] }, { "page": "featureAnnotations-class", "title": "Base feature annotations class", "topics": [ "$,featureAnnotations-method", "annotations,featureAnnotations-method", "as.data.table,featureAnnotations-method", "delete,featureAnnotations-method", "featureAnnotations", "featureAnnotations-class", "filter,featureAnnotations-method", "groupNames,featureAnnotations-method", "length,featureAnnotations-method", "plotUpSet,featureAnnotations-method", "plotVenn,featureAnnotations-method", "[,featureAnnotations,ANY,missing,missing-method", "[[,featureAnnotations,ANY,missing-method" ] }, { "page": "featureGroups-class", "title": "Base class for grouped features.", "topics": [ "$,featureGroups-method", "adducts,featureGroups-method", "adducts,featureGroupsSet-method", "adducts<-,featureGroups-method", "adducts<-,featureGroupsSet-method", "analyses,featureGroups-method", "analysisInfo,featureGroups-method", "analysisInfo<-,featureGroups-method", "analysisInfo<-,featureGroupsXCMS-method", "annotations,featureGroups-method", "calculatePeakQualities,featureGroups-method", "concentrations", "concentrations,featureGroups-method", "delete,featureGroups-method", "delete,featureGroupsKPIC2-method", "delete,featureGroupsSet-method", "delete,featureGroupsXCMS-method", "delete,featureGroupsXCMS3-method", "export,featureGroups-method", "export,featureGroupsSet-method", "featureGroups", "featureGroups-class", "featureGroupsBruker", "featureGroupsBruker-class", "featureGroupsEnviMass", "featureGroupsEnviMass-class", "featureGroupsGreedy", "featureGroupsGreedy-class", "featureGroupsIMS", "featureGroupsIMS-class", "featureGroupsKPIC2", "featureGroupsKPIC2-class", "featureGroupsOpenMS", "featureGroupsOpenMS-class", "featureGroupsSet", "featureGroupsSet-class", "featureGroupsSIRIUS", "featureGroupsSIRIUS-class", "featureGroupsTable", "featureGroupsTable-class", "featureGroupsUnset", "featureGroupsUnset-class", "featureGroupsXCMS", "featureGroupsXCMS-class", "featureGroupsXCMS3", "featureGroupsXCMS3-class", "featureTable,featureGroups-method", "featureTable,featureGroupsSet-method", "fromIMS,featureGroups-method", "getBPCs,featureGroups-method", "getFeatureQualityNames,featureGroups-method", "getFeatures,featureGroups-method", "getTICs,featureGroups-method", "groupFeatIndex", "groupFeatIndex,featureGroups-method", "groupInfo", "groupInfo,featureGroups-method", "groupNames,featureGroups-method", "groupQualities", "groupQualities,featureGroups-method", "groupScores", "groupScores,featureGroups-method", "groupTable", "groupTable,featureGroups-method", "hasIMS,featureGroups-method", "internalStandardAssignments", "internalStandardAssignments,featureGroups-method", "internalStandardAssignments,featureGroupsSet-method", "internalStandards", "internalStandards,featureGroups-method", "length,featureGroups-method", "names,featureGroups-method", "normInts", "normInts,featureGroups-method", "normInts,featureGroupsSet-method", "overlap", "overlap,featureGroups-method", "replicates,featureGroups-method", "selectIons", "selectIons,featureGroups-method", "selectIons,featureGroupsSet-method", "sets,featureGroupsSet-method", "show,featureGroups-method", "show,featureGroupsSet-method", "toxicities", "toxicities,featureGroups-method", "unique", "unique,featureGroups-method", "unset,featureGroupsSet-method", "updateGroups", "updateGroups,featureGroups-method", "[,featureGroups,ANY,ANY,missing-method", "[,featureGroupsSet,ANY,ANY,missing-method", "[[,featureGroups,ANY,ANY-method" ] }, { "page": "featureGroups-compare", "title": "Comparing feature groups", "topics": [ "comparison", "comparison,featureGroups-method", "comparison,featureGroupsSet-method", "consensus,featureGroupsComparison-method", "consensus,featureGroupsComparisonSet-method", "featureGroups-compare", "featureGroupsConsensus", "featureGroupsConsensus-class", "featuresConsensus", "featuresConsensus-class", "featuresFromFeatGroups", "featuresFromFeatGroups-class", "hasIMS,featureGroupsComparison-method", "plot,featureGroupsComparison,missing-method", "plotChord,featureGroupsComparison-method", "plotUpSet,featureGroupsComparison-method", "plotVenn,featureGroupsComparison-method" ] }, { "page": "featureGroupsComparison-class", "title": "Feature groups comparison class", "topics": [ "$,featureGroupsComparison-method", "featureGroupsComparison", "featureGroupsComparison-class", "featureGroupsComparisonSet", "featureGroupsComparisonSet-class", "length,featureGroupsComparison-method", "names,featureGroupsComparison-method", "[,featureGroupsComparison,ANY,missing,missing-method", "[[,featureGroupsComparison,ANY,missing-method" ] }, { "page": "featureGroupsScreening-class", "title": "Class for suspect screened feature groups.", "topics": [ "delete,featureGroupsScreening-method", "delete,featureGroupsScreeningSet-method", "featureGroupsScreening", "featureGroupsScreening-class", "featureGroupsScreeningSet", "featureGroupsScreeningSet-class", "featureGroupsSetScreeningUnset", "featureGroupsSetScreeningUnset-class", "filter,featureGroupsScreening-method", "filter,featureGroupsScreeningSet-method", "screenInfo", "screenInfo,featureGroupsScreening-method", "screenInfo,featureGroupsScreeningSet-method", "show,featureGroupsScreening-method", "show,featureGroupsScreeningSet-method", "unset,featureGroupsScreeningSet-method", "[,featureGroupsScreening,ANY,ANY,missing-method", "[,featureGroupsScreeningSet,ANY,ANY,missing-method" ] }, { "page": "features-class", "title": "Base features class", "topics": [ "$,features-method", "analyses,features-method", "analysisInfo,features-method", "analysisInfo<-,features-method", "analysisInfo<-,featuresXCMS-method", "as.data.table,features-method", "as.data.table,featuresSet-method", "calculatePeakQualities,features-method", "delete,features-method", "delete,featuresKPIC2-method", "delete,featuresPiek-method", "delete,featuresXCMS-method", "delete,featuresXCMS3-method", "features", "features-class", "featuresBruker", "featuresBruker-class", "featuresEnviPick", "featuresEnviPick-class", "featuresKPIC2", "featuresKPIC2-class", "featuresOpenMS", "featuresOpenMS-class", "featuresPiek", "featuresPiek-class", "featuresSAFD", "featuresSAFD-class", "featuresSet", "featuresSet-class", "featuresSIRIUS", "featuresSIRIUS-class", "featuresTable", "featuresTable-class", "featuresUnset", "featuresUnset-class", "featuresXCMS", "featuresXCMS-class", "featuresXCMS3", "featuresXCMS3-class", "featureTable,features-method", "filter,features-method", "filter,featuresSet-method", "fromIMS,features-method", "getBPCs,features-method", "getFeatureQualityNames,features-method", "getTICs,features-method", "hasIMS,features-method", "length,features-method", "plotBPCs,features-method", "plotTICs,features-method", "replicates,features-method", "sets,featuresSet-method", "show,features-method", "show,featuresSet-method", "unset,featuresSet-method", "[,features,ANY,missing,missing-method", "[,featuresSet,ANY,missing,missing-method", "[[,features,ANY,missing-method" ] }, { "page": "findFeatures", "title": "Finding features", "topics": [ "findFeatures" ] }, { "page": "findFeaturesBruker", "title": "Find features using Bruker DataAnalysis", "topics": [ "findFeaturesBruker" ] }, { "page": "findFeaturesEnviPick", "title": "Find features using enviPick", "topics": [ "findFeaturesEnviPick" ] }, { "page": "findFeaturesKPIC2", "title": "Find features using KPIC2", "topics": [ "findFeaturesKPIC2" ] }, { "page": "findFeaturesOpenMS", "title": "Find features using OpenMS", "topics": [ "findFeaturesOpenMS" ] }, { "page": "findFeaturesPiek", "title": "Find features using piek", "topics": [ "findFeaturesPiek", "getPiekEICParams" ] }, { "page": "findFeaturesSAFD", "title": "Find features using SAFD", "topics": [ "findFeaturesSAFD" ] }, { "page": "findFeaturesSIRIUS", "title": "Find features using SIRIUS", "topics": [ "findFeaturesSIRIUS" ] }, { "page": "findFeaturesXCMS", "title": "Find features using XCMS (old interface)", "topics": [ "findFeaturesXCMS" ] }, { "page": "findFeaturesXCMS3", "title": "Find features using XCMS (new interface)", "topics": [ "findFeaturesXCMS3" ] }, { "page": "formulas-class", "title": "Formula annotations class", "topics": [ "analyses,formulas-method", "annotatedPeakList,formulas-method", "annotatedPeakList,formulasSet-method", "annotations,formulas-method", "as.data.table,formulas-method", "consensus,formulas-method", "consensus,formulasSet-method", "defaultExclNormScores,formulas-method", "delete,formulas-method", "delete,formulasSet-method", "delete,formulasSIRIUS-method", "filter,formulasSet-method", "formulas", "formulas-class", "formulasConsensus", "formulasConsensus-class", "formulasConsensusSet", "formulasConsensusSet-class", "formulasSet", "formulasSet-class", "formulasUnset", "formulasUnset-class", "plotScores,formulas-method", "plotSpectrum,formulas-method", "plotSpectrum,formulasSet-method", "show,formulas-method", "show,formulasSet-method", "unset,formulasConsensusSet-method", "unset,formulasSet-method", "[,formulasSet,ANY,missing,missing-method", "[[,formulas,ANY,ANY-method" ] }, { "page": "formulaScorings", "title": "Scorings terms for formula candidates", "topics": [ "formulaScorings" ] }, { "page": "formulasSIRIUS-class", "title": "Formulas class for SIRIUS results.", "topics": [ "formulasSIRIUS", "formulasSIRIUS-class" ] }, { "page": "generateComponents", "title": "Grouping feature groups in components", "topics": [ "generateComponents", "generateComponents,featureGroups-method" ] }, { "page": "generateComponentsCAMERA", "title": "Componentization of adducts, isotopes etc. with CAMERA", "topics": [ "generateComponentsCAMERA", "generateComponentsCAMERA,featureGroups-method", "generateComponentsCAMERA,featureGroupsSet-method" ] }, { "page": "generateComponentsCliqueMS", "title": "Componentization of adducts, isotopes etc. with cliqueMS", "topics": [ "generateComponentsCliqueMS", "generateComponentsCliqueMS,featureGroups-method", "generateComponentsCliqueMS,featureGroupsSet-method" ] }, { "page": "generateComponentsIntClust", "title": "Generate components based on intensity profiles", "topics": [ "generateComponentsIntClust", "generateComponentsIntClust,featureGroups-method" ] }, { "page": "generateComponentsNontarget", "title": "Componentization of homologous series with nontarget", "topics": [ "generateComponentsNontarget", "generateComponentsNontarget,featureGroups-method", "generateComponentsNontarget,featureGroupsSet-method" ] }, { "page": "generateComponentsOpenMS", "title": "Componentization of adducts, isotopes etc. with OpenMS", "topics": [ "generateComponentsOpenMS", "generateComponentsOpenMS,featureGroups-method", "generateComponentsOpenMS,featureGroupsSet-method" ] }, { "page": "generateComponentsRAMClustR", "title": "Componentization of adducts, isotopes etc. with RAMClustR", "topics": [ "generateComponentsRAMClustR", "generateComponentsRAMClustR,featureGroups-method", "generateComponentsRAMClustR,featureGroupsSet-method" ] }, { "page": "generateComponentsSpecClust", "title": "Generate components based on MS/MS similarity", "topics": [ "generateComponentsSpecClust", "generateComponentsSpecClust,featureGroups-method" ] }, { "page": "generateComponentsTPs", "title": "Generate components of transformation products", "topics": [ "generateComponentsTPs", "generateComponentsTPs,featureGroups-method", "generateComponentsTPs,featureGroupsSet-method" ] }, { "page": "generateCompounds", "title": "Automatic compound annotation", "topics": [ "generateCompounds", "generateCompounds,featureGroups-method" ] }, { "page": "generateCompoundsLibrary", "title": "Compound annotation with an MS library", "topics": [ "generateCompoundsLibrary", "generateCompoundsLibrary,featureGroups-method", "generateCompoundsLibrary,featureGroupsSet-method" ] }, { "page": "generateCompoundsMetFrag", "title": "Compound annotation with MetFrag", "topics": [ "generateCompoundsMetFrag", "generateCompoundsMetFrag,featureGroups-method", "generateCompoundsMetFrag,featureGroupsSet-method" ] }, { "page": "generateCompoundsSIRIUS", "title": "Compound annotation with SIRIUS", "topics": [ "generateCompoundsSIRIUS", "generateCompoundsSIRIUS,featureGroups-method", "generateCompoundsSIRIUS,featureGroupsSet-method" ] }, { "page": "generateFormulas", "title": "Automatic chemical formula generation", "topics": [ "generateFormulas", "generateFormulas,featureGroups-method" ] }, { "page": "generateFormulasGenForm", "title": "Generate formula with GenForm", "topics": [ "generateFormulasGenForm", "generateFormulasGenForm,featureGroups-method", "generateFormulasGenForm,featureGroupsSet-method" ] }, { "page": "generateFormulasSIRIUS", "title": "Generate formula with SIRIUS", "topics": [ "generateFormulasSIRIUS", "generateFormulasSIRIUS,featureGroups-method", "generateFormulasSIRIUS,featureGroupsSet-method" ] }, { "page": "generateMSPeakLists", "title": "Generation of MS Peak Lists", "topics": [ "generateMSPeakLists", "generateMSPeakLists,featureGroups-method", "generateMSPeakLists,featureGroupsSet-method" ] }, { "page": "generateTPs", "title": "Generation of transformation products (TPs)", "topics": [ "generateTPs" ] }, { "page": "generateTPsAnnComp", "title": "Obtain transformation products (TPs) from compound annotation candidates", "topics": [ "generateTPsAnnComp" ] }, { "page": "generateTPsAnnForm", "title": "Obtain transformation products (TPs) from formula annotation candidates", "topics": [ "generateTPsAnnForm" ] }, { "page": "generateTPsBioTransformer", "title": "Obtain transformation products (TPs) with BioTransformer", "topics": [ "generateTPsBioTransformer" ] }, { "page": "generateTPsCTS", "title": "Obtain transformation products (TPs) with Chemical Transformation Simulator (CTS)", "topics": [ "generateTPsCTS" ] }, { "page": "generateTPsLibrary", "title": "Obtain transformation products (TPs) from a library", "topics": [ "generateTPsLibrary" ] }, { "page": "generateTPsLibraryFormula", "title": "Obtain transformation products (TPs) from a library with formula data", "topics": [ "generateTPsLibraryFormula" ] }, { "page": "generateTPsLogic", "title": "Obtain transformation products (TPs) with metabolic logic", "topics": [ "generateTPsLogic", "generateTPsLogic,featureGroups-method", "generateTPsLogic,featureGroupsSet-method" ] }, { "page": "generics", "title": "Miscellaneous generics", "topics": [ "$", "adducts", "adducts<-", "algorithm", "analyses", "analysisInfo", "analysisInfo<-", "annotatedPeakList", "annotations", "as.data.frame", "as.data.table", "assignMobilities", "calculatePeakQualities", "clusterProperties", "clusters", "consensus", "convertToMFDB", "convertToSuspects", "cutClusters", "defaultExclNormScores", "delete", "export", "featureTable", "filter", "fromIMS", "generics", "getBPCs", "getFeatureQualityNames", "getFeatures", "getMCS", "getTICs", "groupNames", "hasIMS", "length", "lengths", "names", "plot", "plotBPCs", "plotChord", "plotChroms", "plotChroms3D", "plotGraph", "plotInt", "plotScores", "plotSilhouettes", "plotSpectrum", "plotStructure", "plotTICs", "plotUpSet", "plotVenn", "plotVolcano", "predictRespFactors", "predictTox", "replicates", "setObjects", "sets", "show", "treeCut", "treeCutDynamic", "unset", "[", "[[" ] }, { "page": "genFormulaTPLibrary", "title": "Automatically generate a transformation product library with formula data.", "topics": [ "genFormulaTPLibrary" ] }, { "page": "getBGMSMSPeaks", "title": "Background MS/MS peak detection", "topics": [ "getBGMSMSPeaks" ] }, { "page": "getCCSParams", "title": "Parameters for CCS calculation", "topics": [ "getCCSParams" ] }, { "page": "getDefAvgPListParams", "title": "Parameters for averaging MS peak list data", "topics": [ "getDefAvgPListParams" ] }, { "page": "getDefPeakParams", "title": "Peak detection parameters", "topics": [ "getDefPeakParams" ] }, { "page": "getDefTPStructParams", "title": "Parameters to handle TP data with structural information", "topics": [ "getDefTPStructParams" ] }, { "page": "getEICs", "title": "Obtains extracted ion chromatograms (EICs)", "topics": [ "getEICs" ] }, { "page": "getFCParams", "title": "Fold change calculation", "topics": [ "getFCParams" ] }, { "page": "getIMSMatchParams", "title": "Parameters for IMS matching", "topics": [ "getIMSMatchParams" ] }, { "page": "getIMSRangeParams", "title": "Parameters to specify a IMS data range", "topics": [ "getIMSRangeParams" ] }, { "page": "getMSFileFormats", "title": "Get supported MS file formats", "topics": [ "getMSFileFormats" ] }, { "page": "getMSFileTypes", "title": "Get supported MS file types", "topics": [ "getMSFileTypes" ] }, { "page": "groupFeatures", "title": "Grouping of features", "topics": [ "groupFeatures", "groupFeatures,data.frame-method", "groupFeatures,features-method" ] }, { "page": "groupFeaturesGreedy", "title": "Group features using greedy algorithm", "topics": [ "groupFeaturesGreedy", "groupFeaturesGreedy,features-method" ] }, { "page": "groupFeaturesKPIC2", "title": "Group features using KPIC2", "topics": [ "groupFeaturesKPIC2", "groupFeaturesKPIC2,features-method", "groupFeaturesKPIC2,featuresSet-method" ] }, { "page": "groupFeaturesOpenMS", "title": "Group features using OpenMS", "topics": [ "groupFeaturesOpenMS", "groupFeaturesOpenMS,features-method" ] }, { "page": "groupFeaturesSIRIUS", "title": "Group features using SIRIUS", "topics": [ "groupFeaturesSIRIUS" ] }, { "page": "groupFeaturesXCMS", "title": "Group features using XCMS (old interface)", "topics": [ "groupFeaturesXCMS", "groupFeaturesXCMS,features-method", "groupFeaturesXCMS,featuresSet-method" ] }, { "page": "groupFeaturesXCMS3", "title": "Group features using XCMS (new interface)", "topics": [ "groupFeaturesXCMS3", "groupFeaturesXCMS3,features-method", "groupFeaturesXCMS3,featuresSet-method" ] }, { "page": "id-conf", "title": "Identification confidence estimation", "topics": [ "estimateIDConfidence", "estimateIDConfidence,compounds-method", "estimateIDConfidence,compoundsSet-method", "estimateIDConfidence,featureGroupsScreening-method", "estimateIDConfidence,featureGroupsScreeningSet-method", "estimateIDConfidence,formulas-method", "estimateIDConfidence,formulasSet-method", "genIDLevelRulesFile", "id-conf", "numericIDLevel" ] }, { "page": "importFeatureGroups", "title": "Import feature groups from files", "topics": [ "importFeatureGroups" ] }, { "page": "importFeatureGroupsBrukerPA", "title": "Imports feature groups from Bruker ProfileAnalysis", "topics": [ "importFeatureGroupsBrukerPA" ] }, { "page": "importFeatureGroupsBrukerTASQ", "title": "Imports feature groups from Bruker TASQ", "topics": [ "featureGroupsBrukerTASQ", "featuresBrukerTASQ", "featuresBrukerTASQ-class", "importFeatureGroupsBrukerTASQ" ] }, { "page": "importFeatureGroupsEnviMass", "title": "Imports feature groups from enviMass", "topics": [ "importFeatureGroupsEnviMass" ] }, { "page": "importFeatureGroupsKPIC2", "title": "Imports feature groups from KPIC2", "topics": [ "importFeatureGroupsKPIC2" ] }, { "page": "importFeatureGroupsTable", "title": "Import feature groups from a table", "topics": [ "importFeatureGroupsTable" ] }, { "page": "importFeatureGroupsXCMS", "title": "Imports feature groups from XCMS (old interface)", "topics": [ "importFeatureGroupsXCMS" ] }, { "page": "importFeatureGroupsXCMS3", "title": "Imports feature groups from XCMS (new interface)", "topics": [ "importFeatureGroupsXCMS3" ] }, { "page": "importFeatures", "title": "Import features", "topics": [ "importFeatures" ] }, { "page": "importFeaturesEnviMass", "title": "Imports features from enviMass", "topics": [ "importFeaturesEnviMass" ] }, { "page": "importFeaturesKPIC2", "title": "Imports features from KPIC2", "topics": [ "importFeaturesKPIC2" ] }, { "page": "importFeaturesTable", "title": "Import features from a table", "topics": [ "importFeaturesTable" ] }, { "page": "importFeaturesXCMS", "title": "Imports features from XCMS (old interface)", "topics": [ "importFeaturesXCMS" ] }, { "page": "importFeaturesXCMS3", "title": "Imports features from XCMS (new interface)", "topics": [ "importFeaturesXCMS3" ] }, { "page": "installC3SDB", "title": "Automatically installs C3SDB", "topics": [ "installC3SDB" ] }, { "page": "installTIMSCONVERT", "title": "Automatically installs TIMSCONVERT", "topics": [ "installTIMSCONVERT" ] }, { "page": "kpic2-conv", "title": "Conversion to KPIC2 objects", "topics": [ "getPICSet", "getPICSet,features-method", "getPICSet,featuresKPIC2-method", "kpic2-conv" ] }, { "page": "launchEICGUI", "title": "Launch EIC/EIM GUI", "topics": [ "launchEICGUI", "launchEICGUI,featureGroups-method", "launchEICGUI,features-method" ] }, { "page": "limits", "title": "Default limits and tolerances", "topics": [ "defaultLim", "genLimitsFile", "getLimIMS", "limits" ] }, { "page": "loadMSLibrary", "title": "Loading of MS library data", "topics": [ "loadMSLibrary" ] }, { "page": "loadMSLibraryMoNAJSON", "title": "Load MS library data from MassBank of North America (MoNA)", "topics": [ "loadMSLibraryMoNAJSON" ] }, { "page": "loadMSLibraryMSP", "title": "Load MS library data from MSP files", "topics": [ "loadMSLibraryMSP" ] }, { "page": "makeSet", "title": "Initiate sets workflows", "topics": [ "makeSet", "makeSet,featureGroups-method", "makeSet,featureGroupsSet-method", "makeSet,features-method", "makeSet,featuresSet-method" ] }, { "page": "MSConversion", "title": "MS data conversion", "topics": [ "convertMSFiles", "convertMSFilesBruker", "convertMSFilesIMSCollapse", "convertMSFilesOpenMS", "convertMSFilesPaths", "convertMSFilesPWiz", "convertMSFilesTIMSCONVERT", "getMSConversionFormats", "getMSConversionTypes", "MSConversion" ] }, { "page": "msdata", "title": "Interface for HRMS and IMS-HRMS raw data", "topics": [ "availableBackends", "msdata" ] }, { "page": "MSLibrary-class", "title": "Class to store data from a loaded MS library", "topics": [ "$,MSLibrary-method", "as.data.table,MSLibrary-method", "convertToSuspects,MSLibrary-method", "delete,MSLibrary-method", "export,MSLibrary-method", "filter,MSLibrary-method", "length,MSLibrary-method", "merge,MSLibrary,MSLibrary-method", "MSLibrary", "MSLibrary-class", "names,MSLibrary-method", "records", "records,MSLibrary-method", "show,MSLibrary-method", "spectra", "spectra,MSLibrary-method", "[,MSLibrary,ANY,missing,missing-method", "[[,MSLibrary,ANY,missing-method" ] }, { "page": "MSPeakLists-class", "title": "Class containing MS Peak Lists", "topics": [ "$,MSPeakLists-method", "analyses,MSPeakLists-method", "analysisInfo,MSPeakListsSet-method", "as.data.table,MSPeakLists-method", "as.data.table,MSPeakListsSet-method", "averagedPeakLists", "averagedPeakLists,MSPeakLists-method", "delete,MSPeakLists-method", "delete,MSPeakListsSet-method", "filter,MSPeakLists-method", "filter,MSPeakListsSet-method", "getDefIsolatePrecParams", "groupNames,MSPeakLists-method", "length,MSPeakLists-method", "MSPeakLists", "MSPeakLists-class", "MSPeakListsSet", "MSPeakListsSet-class", "MSPeakListsUnset", "MSPeakListsUnset-class", "peakLists", "peakLists,MSPeakLists-method", "plotSpectrum,MSPeakLists-method", "plotSpectrum,MSPeakListsSet-method", "show,MSPeakLists-method", "show,MSPeakListsSet-method", "spectrumSimilarity", "spectrumSimilarity,MSPeakLists-method", "spectrumSimilarity,MSPeakListsSet-method", "spectrumSimilarityIMS", "spectrumSimilarityIMS,MSPeakLists-method", "unset,MSPeakListsSet-method", "[,MSPeakLists,ANY,ANY,missing-method", "[,MSPeakListsSet,ANY,ANY,missing-method", "[[,MSPeakLists,ANY,ANY-method" ] }, { "page": "newProject", "title": "Easily create new 'patRoon' projects", "topics": [ "newProject" ] }, { "page": "optimizationResult-class", "title": "Class containing optimization results.", "topics": [ "algorithm,optimizationResult-method", "experimentInfo", "experimentInfo,optimizationResult-method", "length,optimizationResult-method", "lengths,optimizationResult-method", "optimizationResult", "optimizationResult-class", "optimizedObject", "optimizedObject,optimizationResult-method", "optimizedParameters", "optimizedParameters,optimizationResult-method", "plot,optimizationResult,missing-method", "scores", "scores,optimizationResult-method", "show,optimizationResult-method" ] }, { "page": "pred-aggr-params", "title": "Parameters to aggregate concentrations/toxicity values assigned to feature groups", "topics": [ "getDefPredAggrParams", "pred-aggr-params" ] }, { "page": "pred-quant", "title": "Functionality to predict quantitative data", "topics": [ "calculateConcs", "calculateConcs,featureGroups-method", "calculateConcs,featureGroupsScreening-method", "calculateConcs,featureGroupsScreeningSet-method", "calculateConcs,featureGroupsSet-method", "getQuantCalibFromScreening", "pred-quant", "predictRespFactors,compounds-method", "predictRespFactors,compoundsSet-method", "predictRespFactors,compoundsSIRIUS-method", "predictRespFactors,featureGroupsScreening-method", "predictRespFactors,featureGroupsScreeningSet-method", "predictRespFactors,formulasSet-method", "predictRespFactors,formulasSIRIUS-method" ] }, { "page": "pred-tox", "title": "Functionality to predict toxicities", "topics": [ "calculateTox", "calculateTox,featureGroups-method", "calculateTox,featureGroupsScreening-method", "calculateTox,featureGroupsScreeningSet-method", "calculateTox,featureGroupsSet-method", "pred-tox", "predictTox,compounds-method", "predictTox,compoundsSet-method", "predictTox,compoundsSIRIUS-method", "predictTox,featureGroupsScreening-method", "predictTox,featureGroupsScreeningSet-method", "predictTox,formulasSet-method", "predictTox,formulasSIRIUS-method" ] }, { "page": "printPackageOpts", "title": "Prints all the package options of 'patRoon' and their currently set values.", "topics": [ "printPackageOpts" ] }, { "page": "reporting", "title": "Report workflow data", "topics": [ "genReportSettingsFile", "report", "report,featureGroups-method", "reporting" ] }, { "page": "reporting-legacy", "title": "Report feature group data (legacy interface)", "topics": [ "reportCSV", "reportCSV,featureGroups-method", "reporting-legacy", "reportPDF", "reportPDF,featureGroups-method" ] }, { "page": "retDir", "title": "Retention order direction", 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