Package: patRoon 2.3.3
patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Authors:
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patRoon.pdf |patRoon.html✨
patRoon/json (API)
NEWS
| # Install 'patRoon' in R: |
| install.packages('patRoon', repos = c('https://rickhelmus.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rickhelmus/patroon/issues
Last updated 4 hours agofrom:933849be4e. Checks:ERROR: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 21 2024 |
| R-4.5-win-x86_64 | ERROR | Nov 21 2024 |
| R-4.5-linux-x86_64 | ERROR | Nov 21 2024 |
| R-4.4-win-x86_64 | ERROR | Nov 21 2024 |
| R-4.4-mac-x86_64 | ERROR | Nov 21 2024 |
| R-4.4-mac-aarch64 | ERROR | Nov 21 2024 |
| R-4.3-win-x86_64 | ERROR | Nov 21 2024 |
| R-4.3-mac-x86_64 | ERROR | Nov 21 2024 |
| R-4.3-mac-aarch64 | ERROR | Oct 22 2024 |
Exports:addAllDAEICsaddDAEICaddFormulaScoringadductadductsadducts<-algorithmanalysesanalysisInfoannotatedPeakListannotateSuspectsannotationsas.adductas.data.frameas.data.tableaveragedPeakListscalculateConcscalculateIonFormulacalculateNeutralFormulacalculatePeakQualitiescalculateToxcheckChromatogramscheckComponentscheckFeaturesclearCacheclusterPropertiesclusterscomparisoncomponentInfocomponentscomponentsCameracomponentsCliqueMScomponentsClustcomponentsFeaturescomponentsIntClustcomponentsNTcomponentsNTSetcomponentsNTUnsetcomponentsOpenMScomponentsSetcomponentsSpecClustcomponentsTPscomponentsUnsetcomponentTablecompoundscompoundsClustercompoundsConsensusSetcompoundScoringscompoundsMFcompoundsSetcompoundsSIRIUScompoundsUnsetcompoundTablecompoundViewerCOMStopconcentrationsconsensusconvertMSFilesconvertToMFDBconvertToSuspectscreateCOMReferencecutClustersdefaultExclNormScoresdefaultOpenMSAdductsdeleteexperimentInfoexportexportDAFilesfeatureAnnotationsfeatureGroupsfeatureGroupsBrukerfeatureGroupsComparisonfeatureGroupsComparisonSetfeatureGroupsConsensusfeatureGroupsEnviMassfeatureGroupsKPIC2featureGroupsOpenMSfeatureGroupsScreeningfeatureGroupsScreeningSetfeatureGroupsSetfeatureGroupsSetScreeningUnsetfeatureGroupsSIRIUSfeatureGroupsUnsetfeatureGroupsXCMSfeatureGroupsXCMS3featureQualityNamesfeaturesfeaturesBrukerfeaturesConsensusfeaturesEnviPickfeaturesKPIC2featuresOpenMSfeaturesSAFDfeaturesSetfeaturesSIRIUSfeaturesUnsetfeaturesXCMSfeaturesXCMS3featureTablefilterfindFeaturesfindFeaturesBrukerfindFeaturesEnviPickfindFeaturesKPIC2findFeaturesOpenMSfindFeaturesSAFDfindFeaturesSIRIUSfindFeaturesXCMSfindFeaturesXCMS3findFGroupformulasformulasConsensusSetformulaScoringsformulasSetformulasSIRIUSformulasUnsetformulaTablegenerateAnalysisInfogenerateAnalysisInfoFromEnviMassgenerateComponentsgenerateComponentsCAMERAgenerateComponentsCliqueMSgenerateComponentsIntClustgenerateComponentsNontargetgenerateComponentsOpenMSgenerateComponentsRAMClustRgenerateComponentsSpecClustgenerateComponentsTPsgenerateCompoundsgenerateCompoundsLibrarygenerateCompoundsMetFraggenerateCompoundsSIRIUSgenerateFeatureOptPSetgenerateFGroupsOptPSetgenerateFormulasgenerateFormulasDAgenerateFormulasGenFormgenerateFormulasSIRIUSgenerateMSPeakListsgenerateMSPeakListsDAgenerateMSPeakListsDAFMFgenerateMSPeakListsMzRgenerateTPsgenerateTPsBioTransformergenerateTPsCTSgenerateTPsLibrarygenerateTPsLibraryFormulagenerateTPsLogicGenFormAdductsgenFormulaTPLibrarygenIDLevelRulesFilegenReportSettingsFilegetBPCsgetDACalibrationErrorgetDefAvgPListParamsgetDefEICParamsgetDefFeaturesOptParamRangesgetDefFGroupsOptParamRangesgetDefIsolatePrecParamsgetDefPredAggrParamsgetDefSpecSimParamsgetEICsgetFCParamsgetFeaturesgetMCSgetMCTrainDatagetPICSetgetQuantCalibFromScreeninggetTICsgetXCMSnExpgetXCMSSetgroupFeatIndexgroupFeaturesgroupFeaturesKPIC2groupFeaturesOpenMSgroupFeaturesScreeninggroupFeaturesSIRIUSgroupFeaturesXCMSgroupFeaturesXCMS3groupInfogroupNamesgroupQualitiesgroupsgroupScoresgroupTableidentifiersimportCheckFeaturesSessionimportFeatureGroupsimportFeatureGroupsBrukerPAimportFeatureGroupsBrukerTASQimportFeatureGroupsEnviMassimportFeatureGroupsKPIC2importFeatureGroupsXCMSimportFeatureGroupsXCMS3importFeaturesimportFeaturesEnviMassimportFeaturesKPIC2importFeaturesXCMSimportFeaturesXCMS3internalStandardAssignmentsinternalStandardsloadCacheDataloadMSLibraryloadMSLibraryMoNAJSONloadMSLibraryMSPmakeFileHashmakeHashmakeHClustermakeSetmergeMetFragAdductsMSFileFormatsMSLibraryMSPeakListsMSPeakListsSetMSPeakListsUnsetnewProjectnormIntsnumericIDLeveloptimizationResultoptimizedObjectoptimizedParametersoptimizeFeatureFindingoptimizeFeatureGroupingoverlapparentspeakListsplotplotBPCsplotChordplotChromsplotEICplotGraphplotHeatMapplotIntplotScoresplotSilhouettesplotSpecplotSpectrumplotStructureplotTICsplotUpSetplotVennplotVolcanopredictCheckFeaturesSessionpredictRespFactorspredictToxprintPackageOptsproductsrecalibrarateDAFilesrecordsreplicateGroupsreplicateGroupSubtractreportreportCSVreportHTMLreportMDreportPDFrevertDAAnalysessaveCacheDatascoresscreenInfoscreenSuspectsselectIonssetDAMethodsetObjectssetssettingsshowshowDataAnalysisspectraspectrumSimilaritytoxicitiestransformationProductstransformationProductsFormulatransformationProductsLogictransformationProductsStructuretreeCuttreeCutDynamicuniqueunsetverifyDependencieswithOptworkflowStepworkflowStepSet
Dependencies:abindaffyaffyioAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitbit64bitopsblobbslibcacachemcallrCAMERAcaToolscheckmatecirclizecliclueclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydendextenddigestdoParalleldplyrDTdynamicTreeCuteggenviPatestimabilityevaluatefansifarverfastclusterfastmapfingerprintflexdashboardfontawesomeforeachforeignformatRFormulafsfstfstcorefutile.loggerfutile.optionsfuturefuture.applygclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgetPassggplot2GlobalOptionsglobalsgluegplotsgraphgridExtragtablegtoolsheatmaplyhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphimputeIRangesisobanditeratorsitertoolsjquerylibjsonlitekableExtraKernSmoothkeysknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvmagickmagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeminiUIMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmennetopensslparallellypcaMethodspermutepillarpkgconfigplogrplotlyplyrpngpreprocessCoreprettyunitsprocessxprogresspromisesProtGenericspsPSMatchpurrrqapQFeaturesR.methodsS3R.ooR.utilsR6rapidjsonrrappdirsRBGLrbibutilsrcdkrcdklibsRColorBrewerRcppRdpackreactablereactRregistryreshape2rhandsontableRhdf5librJavarlangrmarkdownrpartrsmRSQLiterstudioapiS4ArraysS4VectorssassscalesseriationshapeshinyshinyjssnowsourcetoolsSparseArraySpectrastatmodstringistringrSummarizedExperimentsvglitesyssystemfontstibbletidyrtidyselecttinytexTSPUCSC.utilsUpSetRutf8vctrsveganVennDiagramviridisviridisLitevisNetworkvsnwebshotwithrxcmsxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Workflow solutions for mass-spectrometry based non-target analysis. | patRoon-package patRoon |
| Compound annotations class | 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 |
| Generic adduct class | adduct adduct-class as.character,adduct-method show,adduct-method |
| Adduct utilities | adduct-utils as.adduct calculateIonFormula calculateNeutralFormula GenFormAdducts MetFragAdducts |
| Properties of sample analyses | analysis-information generateAnalysisInfo generateAnalysisInfoFromEnviMass |
| AnalysisInfo data.frame methods | analysisinfo-dataframe getBPCs,data.frame-method getTICs,data.frame-method plotBPCs,data.frame-method plotTICs,data.frame-method |
| Bruker DataAnalysis utilities | addAllDAEICs addDAEIC bruker-utils getDACalibrationError recalibrarateDAFiles revertDAAnalyses setDAMethod showDataAnalysis |
| Utilities for caching of workflow data. | caching clearCache loadCacheData makeFileHash makeHash saveCacheData |
| Interactive GUI utilities to check workflow data | check-GUI checkComponents checkComponents,components-method checkFeatures checkFeatures,featureGroups-method getMCTrainData importCheckFeaturesSession predictCheckFeaturesSession |
| Comparing feature groups | comparison comparison,featureGroups-method comparison,featureGroupsSet-method consensus,featureGroupsComparison-method consensus,featureGroupsComparisonSet-method featureGroups-compare featureGroupsConsensus featureGroupsConsensus-class featuresConsensus featuresConsensus-class featuresFromFeatGroups featuresFromFeatGroups-class plot,featureGroupsComparison,missing-method plotChord,featureGroupsComparison-method plotUpSet,featureGroupsComparison-method plotVenn,featureGroupsComparison-method |
| Base class for components that are based on hierarchical clustered data. | 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 |
| Components class for homologous series. | componentsNT componentsNT-class componentsNTSet componentsNTSet-class componentsNTUnset componentsNTUnset-class plotGraph,componentsNT-method plotGraph,componentsNTSet-method unset,componentsNTSet-method |
| Components based on MS/MS similarity. | componentsSpecClust componentsSpecClust-class |
| Components based on parent and transformation product (TP) linkage. | as.data.table,componentsTPs-method componentsTPs componentsTPs-class filter,componentsTPs-method plotGraph,componentsTPs-method |
| Component class | $,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 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 |
| Compounds cluster class | 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 |
| Scorings terms for compound candidates | compoundScorings |
| Compounds class for SIRIUS results. | compoundsSIRIUS compoundsSIRIUS-class |
| MS data conversion | convertMSFiles MSFileFormats |
| Default adducts for OpenMS componentization | defaultOpenMSAdducts |
| Extracted Ion Chromatogram parameters | EICParams getDefEICParams |
| Optimization of feature finding and grouping parameters | feature-optimization generateFeatureOptPSet generateFGroupsOptPSet getDefFeaturesOptParamRanges getDefFGroupsOptParamRanges optimizeFeatureFinding optimizeFeatureGrouping |
| Plotting of grouped features | feature-plotting plot,featureGroups,missing-method plotChord,featureGroups-method plotChroms,featureGroups-method plotGraph,featureGroups-method plotGraph,featureGroupsSet-method plotInt,featureGroups-method plotInt,featureGroupsSet-method plotUpSet,featureGroups-method plotVenn,featureGroups-method plotVenn,featureGroupsSet-method plotVolcano,featureGroups-method |
| Base feature annotations class | $,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 |
| Feature groups comparison class | $,featureGroupsComparison-method featureGroupsComparison featureGroupsComparison-class featureGroupsComparisonSet featureGroupsComparisonSet-class length,featureGroupsComparison-method names,featureGroupsComparison-method [,featureGroupsComparison,ANY,missing,missing-method [[,featureGroupsComparison,ANY,missing-method |
| Returns chromatographic peak quality and score names for features and/or feature groups. | featureQualityNames |
| Base features class | $,features-method analyses,features-method analysisInfo,features-method as.data.table,features-method as.data.table,featuresSet-method calculatePeakQualities,features-method delete,features-method delete,featuresKPIC2-method delete,featuresXCMS-method delete,featuresXCMS3-method features features-class featuresBruker featuresBruker-class featuresEnviPick featuresEnviPick-class featuresKPIC2 featuresKPIC2-class featuresOpenMS featuresOpenMS-class featuresSAFD featuresSAFD-class featuresSet featuresSet-class featuresSIRIUS featuresSIRIUS-class featuresUnset featuresUnset-class featuresXCMS featuresXCMS-class featuresXCMS3 featuresXCMS3-class featureTable,features-method filter,features-method filter,featuresSet-method getBPCs,features-method getTICs,features-method length,features-method plotBPCs,features-method plotTICs,features-method replicateGroups,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 |
| Finding features | findFeatures |
| Find features using Bruker DataAnalysis | findFeaturesBruker |
| Find features using enviPick | findFeaturesEnviPick |
| Find features using KPIC2 | findFeaturesKPIC2 |
| Find features using OpenMS | findFeaturesOpenMS |
| Find features using SAFD | findFeaturesSAFD |
| Find features using SIRIUS | findFeaturesSIRIUS |
| Find features using XCMS (old interface) | findFeaturesXCMS |
| Find features using XCMS (new interface) | findFeaturesXCMS3 |
| Formula annotations class | 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 |
| Scorings terms for formula candidates | formulaScorings |
| Formulas class for SIRIUS results. | formulasSIRIUS formulasSIRIUS-class |
| Grouping feature groups in components | generateComponents generateComponents,featureGroups-method |
| Componentization of adducts, isotopes etc. with CAMERA | generateComponentsCAMERA generateComponentsCAMERA,featureGroups-method generateComponentsCAMERA,featureGroupsSet-method |
| Componentization of adducts, isotopes etc. with cliqueMS | generateComponentsCliqueMS generateComponentsCliqueMS,featureGroups-method generateComponentsCliqueMS,featureGroupsSet-method |
| Generate components based on intensity profiles | generateComponentsIntClust generateComponentsIntClust,featureGroups-method |
| Componentization of homologous series with nontarget | generateComponentsNontarget generateComponentsNontarget,featureGroups-method generateComponentsNontarget,featureGroupsSet-method |
| Componentization of adducts, isotopes etc. with OpenMS | generateComponentsOpenMS generateComponentsOpenMS,featureGroups-method generateComponentsOpenMS,featureGroupsSet-method |
| Componentization of adducts, isotopes etc. with RAMClustR | generateComponentsRAMClustR generateComponentsRAMClustR,featureGroups-method generateComponentsRAMClustR,featureGroupsSet-method |
| Generate components based on MS/MS similarity | generateComponentsSpecClust generateComponentsSpecClust,featureGroups-method |
| Generate components of transformation products | generateComponentsTPs generateComponentsTPs,featureGroups-method generateComponentsTPs,featureGroupsSet-method |
| Automatic compound annotation | generateCompounds generateCompounds,featureGroups-method |
| Compound annotation with an MS library | generateCompoundsLibrary generateCompoundsLibrary,featureGroups-method generateCompoundsLibrary,featureGroupsSet-method |
| Compound annotation with MetFrag | generateCompoundsMetFrag generateCompoundsMetFrag,featureGroups-method generateCompoundsMetFrag,featureGroupsSet-method |
| Compound annotation with SIRIUS | generateCompoundsSIRIUS generateCompoundsSIRIUS,featureGroups-method generateCompoundsSIRIUS,featureGroupsSet-method |
| Automatic chemical formula generation | generateFormulas generateFormulas,featureGroups-method |
| Generate formula with Bruker DataAnalysis | generateFormulasDA generateFormulasDA,featureGroups-method generateFormulasDA,featureGroupsSet-method |
| Generate formula with GenForm | generateFormulasGenForm generateFormulasGenForm,featureGroups-method generateFormulasGenForm,featureGroupsSet-method |
| Generate formula with SIRIUS | generateFormulasSIRIUS generateFormulasSIRIUS,featureGroups-method generateFormulasSIRIUS,featureGroupsSet-method |
| Generation of MS Peak Lists | generateMSPeakLists generateMSPeakLists,featureGroups-method |
| Generate peak lists with Bruker DataAnalysis | generateMSPeakListsDA generateMSPeakListsDA,featureGroups-method generateMSPeakListsDA,featureGroupsSet-method |
| Generate peak lists with Bruker DataAnalysis from bruker features | generateMSPeakListsDAFMF generateMSPeakListsDAFMF,featureGroups-method generateMSPeakListsDAFMF,featureGroupsSet-method |
| Generate peak lists with mzR | generateMSPeakListsMzR generateMSPeakListsMzR,featureGroups-method generateMSPeakListsMzR,featureGroupsSet-method |
| Generation of transformation products (TPs) | generateTPs |
| Obtain transformation products (TPs) with BioTransformer | generateTPsBioTransformer |
| Obtain transformation products (TPs) with Chemical Transformation Simulator (CTS) | generateTPsCTS |
| Obtain transformation products (TPs) from a library | generateTPsLibrary |
| Obtain transformation products (TPs) from a library with formula data | generateTPsLibraryFormula |
| Obtain transformation products (TPs) with metabolic logic | generateTPsLogic generateTPsLogic,featureGroups-method generateTPsLogic,featureGroupsSet-method |
| Miscellaneous generics | $ adducts adducts<- algorithm analyses analysisInfo annotatedPeakList annotations as.data.frame as.data.table calculatePeakQualities clusterProperties clusters consensus convertToMFDB convertToSuspects cutClusters defaultExclNormScores delete export featureTable filter generics getBPCs getFeatures getMCS getTICs groupNames length lengths names plot plotBPCs plotChord plotChroms plotGraph plotInt plotScores plotSilhouettes plotSpectrum plotStructure plotTICs plotUpSet plotVenn plotVolcano predictRespFactors predictTox replicateGroups setObjects sets show treeCut treeCutDynamic unset [ [[ |
| Automatically generate a transformation product library with formula data. | genFormulaTPLibrary |
| Parameters for averaging MS peak list data | getDefAvgPListParams |
| Obtains extracted ion chromatograms (EICs) | getEICs |
| Fold change calculation | getFCParams |
| Conversion to KPIC2 objects | getPICSet getPICSet,features-method getPICSet,featuresKPIC2-method |
| Conversion to XCMS objects | getXCMSnExp getXCMSnExp,featureGroups-method getXCMSnExp,featureGroupsSet-method getXCMSnExp,featureGroupsXCMS3-method getXCMSnExp,features-method getXCMSnExp,featuresSet-method getXCMSnExp,featuresXCMS3-method getXCMSSet getXCMSSet,featureGroups-method getXCMSSet,featureGroupsSet-method getXCMSSet,featureGroupsXCMS-method getXCMSSet,features-method getXCMSSet,featuresSet-method getXCMSSet,featuresXCMS-method |
| Grouping of features | groupFeatures groupFeatures,data.frame-method groupFeatures,features-method groupFeatures,featuresSet-method |
| Group features using KPIC2 | groupFeaturesKPIC2 groupFeaturesKPIC2,features-method groupFeaturesKPIC2,featuresSet-method |
| Group features using OpenMS | groupFeaturesOpenMS groupFeaturesOpenMS,features-method |
| Group features using SIRIUS | groupFeaturesSIRIUS |
| Group features using XCMS (old interface) | groupFeaturesXCMS groupFeaturesXCMS,features-method groupFeaturesXCMS,featuresSet-method |
| Group features using XCMS (new interface) | groupFeaturesXCMS3 groupFeaturesXCMS3,features-method groupFeaturesXCMS3,featuresSet-method |
| Base class for grouped features. | $,featureGroups-method adducts,featureGroups-method adducts,featureGroupsSet-method adducts<-,featureGroups-method adducts<-,featureGroupsSet-method analyses,featureGroups-method analysisInfo,featureGroups-method annotations,featureGroups-method as.data.table,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 featureGroupsKPIC2 featureGroupsKPIC2-class featureGroupsOpenMS featureGroupsOpenMS-class featureGroupsSet featureGroupsSet-class featureGroupsSIRIUS featureGroupsSIRIUS-class featureGroupsUnset featureGroupsUnset-class featureGroupsXCMS featureGroupsXCMS-class featureGroupsXCMS3 featureGroupsXCMS3-class featureTable,featureGroups-method featureTable,featureGroupsSet-method getBPCs,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 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 overlap,featureGroupsSet-method plotBPCs,featureGroups-method plotTICs,featureGroups-method replicateGroups,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 unique,featureGroupsSet-method unset,featureGroupsSet-method [,featureGroups,ANY,ANY,missing-method [,featureGroupsSet,ANY,ANY,missing-method [[,featureGroups,ANY,ANY-method |
| Import feature groups from files | importFeatureGroups |
| Imports feature groups from Bruker ProfileAnalysis | importFeatureGroupsBrukerPA |
| Imports feature groups from Bruker TASQ | importFeatureGroupsBrukerTASQ |
| Imports feature groups from enviMass | importFeatureGroupsEnviMass |
| Imports feature groups from KPIC2 | importFeatureGroupsKPIC2 |
| Imports feature groups from XCMS (old interface) | importFeatureGroupsXCMS |
| Imports feature groups from XCMS (new interface) | importFeatureGroupsXCMS3 |
| Import features | importFeatures |
| Imports features from enviMass | importFeaturesEnviMass |
| Imports features from KPIC2 | importFeaturesKPIC2 |
| Imports features from XCMS (old interface) | importFeaturesXCMS |
| Imports features from XCMS (new interface) | importFeaturesXCMS3 |
| Loading of MS library data | loadMSLibrary |
| Load MS library data from MassBank of North America (MoNA) | loadMSLibraryMoNAJSON |
| Load MS library data from MSP files | loadMSLibraryMSP |
| Hierarchical clustering of compounds | compounds-cluster makeHCluster makeHCluster,compounds-method |
| Initiate sets workflows | makeSet makeSet,featureGroups-method makeSet,featureGroupsSet-method makeSet,features-method makeSet,featuresSet-method |
| Easily create new 'patRoon' projects | newProject |
| Class containing optimization results. | 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 |
| Base transformation products (TP) class | $,transformationProducts-method as.data.table,transformationProducts-method convertToSuspects,transformationProducts-method delete,transformationProducts-method filter,transformationProducts-method length,transformationProducts-method names,transformationProducts-method parents parents,transformationProducts-method products products,transformationProducts-method show,transformationProducts-method transformationProducts transformationProducts-class transformationProductsLogic transformationProductsLogic-class [,transformationProducts,ANY,missing,missing-method [[,transformationProducts,ANY,missing-method |
| Class containing MS Peak Lists | $,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 unset,MSPeakListsSet-method [,MSPeakLists,ANY,ANY,missing-method [,MSPeakListsSet,ANY,ANY,missing-method [[,MSPeakLists,ANY,ANY-method |
| Components based on clustered intensity profiles. | componentsIntClust componentsIntClust-class plotHeatMap plotHeatMap,componentsIntClust-method plotInt,componentsIntClust-method |
| Parameters to aggregate concentrations/toxicity values assigned to feature groups | getDefPredAggrParams pred-aggr-params |
| Functionality to predict quantitative data | 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 |
| Functionality to predict toxicities | 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 |
| Prints all the package options of 'patRoon' and their currently set values. | printPackageOpts |
| Class to store data from a loaded MS library | $,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 |
| Filtering of grouped features | feature-filtering filter,featureGroups-method filter,featureGroupsSet-method replicateGroupSubtract replicateGroupSubtract,featureGroups-method |
| Report workflow data | genReportSettingsFile report report,featureGroups-method reporting |
| Report feature group data (legacy interface) | reportCSV reportCSV,featureGroups-method reportHTML reportHTML,featureGroups-method reporting-legacy reportPDF reportPDF,featureGroups-method |
| Class for suspect screened feature groups. | annotateSuspects annotateSuspects,featureGroupsScreening-method annotateSuspects,featureGroupsScreeningSet-method as.data.table,featureGroupsScreening-method as.data.table,featureGroupsScreeningSet-method 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 |
| Target and suspect screening | featureGroupsBrukerTASQ featureGroupsBrukerTASQ-class featuresBrukerTASQ featuresBrukerTASQ-class genIDLevelRulesFile numericIDLevel screenSuspects screenSuspects,featureGroups-method screenSuspects,featureGroupsScreening-method screenSuspects,featureGroupsScreeningSet-method screenSuspects,featureGroupsSet-method suspect-screening |
| Sets workflows | sets-workflow |
| Compounds list class for MetFrag results. | compoundsMF compoundsMF-class settings settings,compoundsMF-method |
| MS spectral similarity calculation parameters | getDefSpecSimParams specSimParams |
| Base transformation products (TP) class with formula information | plotGraph,transformationProductsFormula-method transformationProductsFormula transformationProductsFormula-class transformationProductsLibraryFormula transformationProductsLibraryFormula-class |
| Base transformation products (TP) class with structure information | consensus,transformationProductsStructure-method convertToMFDB,transformationProductsStructure-method filter,transformationProductsStructure-method plotGraph,transformationProductsStructure-method plotUpSet,transformationProductsStructure-method plotVenn,transformationProductsStructure-method transformationProductsBT transformationProductsBT-class transformationProductsCTS transformationProductsCTS-class transformationProductsLibrary transformationProductsLibrary-class transformationProductsStructure transformationProductsStructure-class transformationProductsStructureConsensus transformationProductsStructureConsensus-class |
| Verifies if all dependencies are installed properly and instructs the user if this is not the case. | verifyDependencies |
| Temporarily changes package options | withOpt |
| (Virtual) Base class for all workflow objects. | algorithm,workflowStep-method as.data.frame,workflowStep-method as.data.table,workflowStep-method show,workflowStep-method workflowStep workflowStep-class |
| (Virtual) base class for sets related workflow objects | setObjects,workflowStepSet-method sets,workflowStepSet-method show,workflowStepSet-method workflowStepSet workflowStepSet-class |
