Package: patRoon 3.0.0
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:
patRoon_3.0.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
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
mass-spectrometrynon-targetzlibcppopenmpopenjdk
Last updated from:83ff6d7d03. Checks:12 ERROR, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
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| linux-devel-arm64 | ERROR | 542 | ||
| linux-devel-x86_64 | ERROR | 481 | ||
| source / vignettes | ERROR | 920 | ||
| linux-release-arm64 | ERROR | 531 | ||
| linux-release-x86_64 | ERROR | 523 | ||
| macos-release-arm64 | ERROR | 319 | ||
| macos-release-x86_64 | ERROR | 1003 | ||
| macos-oldrel-arm64 | ERROR | 438 | ||
| macos-oldrel-x86_64 | ERROR | 690 | ||
| windows-devel | ERROR | 727 | ||
| windows-release | ERROR | 792 | ||
| windows-oldrel | ERROR | 719 | ||
| wasm-release | FAIL | 306 |
Exports:addAllDAEICsaddDAEICaddFormulaScoringadductadductsadducts<-algorithmanalysesanalysisInfoanalysisInfo<-annotatedPeakListannotateSuspectsannotationsas.adductas.data.frameas.data.tableassignMobilitiesavailableBackendsaveragedPeakListsC3SDBAdductscalculateConcscalculateIonFormulacalculateNeutralFormulacalculatePeakQualitiescalculateToxcheckComponentscheckFeaturesclearCacheclusterPropertiesclusterscomparisoncomponentInfocomponentscomponentsCameracomponentsCliqueMScomponentsClustcomponentsFeaturescomponentsIntClustcomponentsNTcomponentsNTSetcomponentsNTUnsetcomponentsOpenMScomponentsSetcomponentsSpecClustcomponentsTPscomponentsUnsetcomponentTablecompoundscompoundsClustercompoundsConsensusSetcompoundScoringscompoundsMFcompoundsSetcompoundsSIRIUScompoundsUnsetcompoundViewerCOMStopconcentrationsconsensusconvertCCSToMobilityconvertMobilityToCCSconvertMSFilesconvertMSFilesBrukerconvertMSFilesIMSCollapseconvertMSFilesOpenMSconvertMSFilesPathsconvertMSFilesPWizconvertMSFilesTIMSCONVERTconvertToMFDBconvertToSuspectscreateCOMReferencecutClustersdefaultExclNormScoresdefaultLimdefaultOpenMSAdductsdeleteestimateIDConfidenceexpandForIMSexperimentInfoexportfeatureAnnotationsfeatureGroupQualitiesfeatureGroupsfeatureGroupsBrukerfeatureGroupsComparisonfeatureGroupsComparisonSetfeatureGroupsConsensusfeatureGroupsEnviMassfeatureGroupsGreedyfeatureGroupsIMSfeatureGroupsKPIC2featureGroupsOpenMSfeatureGroupsScreeningfeatureGroupsScreeningSetfeatureGroupsSetfeatureGroupsSetScreeningUnsetfeatureGroupsSIRIUSfeatureGroupsUnsetfeatureGroupsXCMSfeatureGroupsXCMS3featureQualitiesfeatureQualityNamesfeaturesfeaturesBrukerfeaturesConsensusfeaturesEnviPickfeaturesKPIC2featuresOpenMSfeaturesPiekfeaturesSAFDfeaturesSetfeaturesSIRIUSfeaturesUnsetfeaturesXCMSfeaturesXCMS3featureTablefilterfindFeaturesfindFeaturesBrukerfindFeaturesEnviPickfindFeaturesKPIC2findFeaturesOpenMSfindFeaturesPiekfindFeaturesSAFDfindFeaturesSIRIUSfindFeaturesXCMSfindFeaturesXCMS3findFGroupformulasformulasConsensusSetformulaScoringsformulasSetformulasSIRIUSformulasUnsetfromIMSgenerateAnalysisInfogenerateAnalysisInfoFromEnviMassgenerateComponentsgenerateComponentsCAMERAgenerateComponentsCliqueMSgenerateComponentsIntClustgenerateComponentsNontargetgenerateComponentsOpenMSgenerateComponentsRAMClustRgenerateComponentsSpecClustgenerateComponentsTPsgenerateCompoundsgenerateCompoundsLibrarygenerateCompoundsMetFraggenerateCompoundsSIRIUSgenerateFeatureOptPSetgenerateFGroupsOptPSetgenerateFormulasgenerateFormulasDAgenerateFormulasGenFormgenerateFormulasSIRIUSgenerateMSPeakListsgenerateMSPeakListsDAgenerateMSPeakListsDAFMFgenerateMSPeakListsMzRgenerateTPsgenerateTPsAnnCompgenerateTPsAnnFormgenerateTPsBioTransformergenerateTPsCTSgenerateTPsLibrarygenerateTPsLibraryFormulagenerateTPsLogicGenFormAdductsgenFormulaTPLibrarygenIDLevelRulesFilegenLimitsFilegenReportSettingsFilegetBGMSMSPeaksgetBPCsgetCCSParamsgetDACalibrationErrorgetDefAvgPListParamsgetDefEICParamsgetDefEIMParamsgetDefFeaturesOptParamRangesgetDefFGroupsOptParamRangesgetDefIsolatePrecParamsgetDefPeakParamsgetDefPredAggrParamsgetDefSpecSimParamsgetDefTPStructParamsgetEICsgetFCParamsgetFeatureQualityNamesgetFeaturesgetIMSMatchParamsgetIMSRangeParamsgetLimIMSgetMCSgetMCTrainDatagetMSConversionFormatsgetMSConversionTypesgetMSFileFormatsgetMSFileTypesgetPICSetgetPiekEICParamsgetQuantCalibFromScreeninggetTICsgetXCMSnExpgetXCMSSetgroupFeatIndexgroupFeaturesgroupFeaturesGreedygroupFeaturesKPIC2groupFeaturesOpenMSgroupFeaturesSIRIUSgroupFeaturesXCMSgroupFeaturesXCMS3groupInfogroupNamesgroupQualitiesgroupScoresgroupTablehasIMSidentifiersimportCheckFeaturesSessionimportFeatureGroupsimportFeatureGroupsBrukerPAimportFeatureGroupsBrukerTASQimportFeatureGroupsEnviMassimportFeatureGroupsKPIC2importFeatureGroupsTableimportFeatureGroupsXCMSimportFeatureGroupsXCMS3importFeaturesimportFeaturesEnviMassimportFeaturesKPIC2importFeaturesTableimportFeaturesXCMSimportFeaturesXCMS3installC3SDBinstallTIMSCONVERTinternalStandardAssignmentsinternalStandardslaunchEICGUIloadCacheDataloadMSLibraryloadMSLibraryMoNAJSONloadMSLibraryMSPmakeFileHashmakeHashmakeHClustermakeSetmergeMetFragAdductsMSLibraryMSPeakListsMSPeakListsSetMSPeakListsUnsetnewProjectnormIntsnumericIDLeveloptimizationResultoptimizedObjectoptimizedParametersoptimizeFeatureFindingoptimizeFeatureGroupingoverlapparentspeakListsplotplotBPCsplotChordplotChromsplotChroms3DplotGraphplotHeatMapplotIntplotMobilogramsplotScoresplotSilhouettesplotSpectrumplotStructureplotTICsplotUpSetplotVennplotVolcanopredictCheckFeaturesSessionpredictRespFactorspredictToxprintPackageOptsproductsrecalibrarateDAFilesrecordsreplicatesreplicateSubtractreportreportCSVreportHTMLreportPDFrevertDAAnalysessaveCacheDatascoresscreenInfoscreenSuspectsselectIonssetDAMethodsetObjectssetssettingsshowshowDataAnalysisspectraspectrumSimilarityspectrumSimilarityIMStoxicitiesTPLogicTransformationstransformationProductstransformationProductsAnnComptransformationProductsAnnFormtransformationProductsFormulatransformationProductsLogictransformationProductsStructuretreeCuttreeCutDynamicuniqueunsetupdateGroupsverifyDependencieswithOptworkflowStepworkflowStepSet
Dependencies:abindaffyaffyioAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbitbit64bitopsblobbsiconsbslibcacachemcallrCAMERAcaToolscheckmatecirclizecliclueclustercodetoolscolorspacecommonmarkconstructivecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydendextenddiffobjdigestdir.expirydoParalleldplyrdynamicTreeCuteggenviPatestimabilityevaluatefarverfastclusterfastmapfilelockfingerprintfontawesomeforeachforeignformatRFormulafsfstfstcorefutile.loggerfutile.optionsfuturefuture.applygclusgenericsGenomicRangesgetPassggplot2GlobalOptionsglobalsgluegplotsgraphgridExtragtablegtoolsheatmaplyhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphimputeIRangesisobanditeratorsitertoolsjquerylibjsonlitekableExtraKernSmoothkeysknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvlzstringmagickmagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsMBAmemoiseMetaboCoreUtilsmgcvmimeminiUIMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4nlmennetopensslotelparallellypcaMethodspermutepillarpkgconfigplotlyplyrpngpreprocessCoreprettyunitsprocessxprogresspromisesProtGenericspsPSMatchPTModspurrrqapQFeaturesR.methodsS3R.ooR.utilsR6rapidjsonrrappdirsRBGLrbibutilsrcdkrcdklibsRColorBrewerRcppRdpackreactablereactRregistryreshape2rhandsontableRhdf5librJavarlangrmarkdownrpartrsmRSQLiterstudioapiS4ArraysS4VectorsS7sassscalesSeqinfoseriationshapeshinyshinyjssignalsnowsourcetoolsSparseArraySpectrastatmodstringistringrSummarizedExperimentsvglitesyssystemfontstextshapingtibbletidyrtidyselecttinytexTSPUpSetRutf8vctrsveganVennDiagramviridisviridisLitevisNetworkvsnwaldowebshotwithrxcmsxfunXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Workflow solutions for mass-spectrometry based non-target analysis. | patRoon-package patRoon |
| 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 plotBPCs,data.table-method plotTICs,data.frame-method plotTICs,data.table-method |
| Assign IMS data to a 'compounds' object. | assignMobilities,compounds-method assignMobilities,compoundsSet-method assignMobilities_comp |
| Assign Ion Mobility and CCS values to features | assignMobilities,featureGroups-method assignMobilities,featureGroupsScreening-method assignMobilities,featureGroupsScreeningSet-method assignMobilities,featureGroupsSet-method assignMobilities_feat |
| Assign IMS data to suspects | assignMobilities,data.frame-method assignMobilities,data.table-method assignMobilities_susp |
| Bruker DataAnalysis utilities | addAllDAEICs addDAEIC bruker-utils getDACalibrationError recalibrarateDAFiles revertDAAnalyses setDAMethod showDataAnalysis |
| Returns the adducts supported by C3SDB | C3SDBAdducts |
| Utilities for caching of workflow data. | caching clearCache loadCacheData makeFileHash makeHash saveCacheData |
| Conversion between mobility and CCS | CCS-Conversion convertCCSToMobility convertMobilityToCCS |
| Interactive GUI utilities to check workflow data | check-GUI checkComponents checkComponents,components-method checkFeatures checkFeatures,featureGroups-method getMCTrainData importCheckFeaturesSession predictCheckFeaturesSession |
| Clustering parameters | cluster-params |
| 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 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 |
| 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 based on clustered intensity profiles. | componentsIntClust componentsIntClust-class plotHeatMap plotHeatMap,componentsIntClust-method plotInt,componentsIntClust-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 |
| 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 |
| Hierarchical clustering of compounds | compounds-cluster makeHCluster makeHCluster,compounds-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 list class for MetFrag results. | compoundsMF compoundsMF-class settings settings,compoundsMF-method |
| Compounds class for SIRIUS results. | compoundsSIRIUS compoundsSIRIUS-class |
| Default adducts for OpenMS componentization | defaultOpenMSAdducts |
| Extracted Ion Chromatogram and Mobilogram parameters | EIXParams getDefEICParams getDefEIMParams |
| Filtering of grouped features | feature-filtering filter,featureGroups-method filter,featureGroupsSet-method replicateSubtract replicateSubtract,featureGroups-method |
| 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 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 |
| Feature quality definitions and utilities | feature-quality featureGroupQualities featureQualities featureQualityNames |
| Feature group to table conversion | as.data.table,featureGroups-method as.data.table,featureGroupsScreening-method as.data.table,featureGroupsScreeningSet-method feature-table |
| 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 |
| 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 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 |
| 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 hasIMS,featureGroupsComparison-method plot,featureGroupsComparison,missing-method plotChord,featureGroupsComparison-method plotUpSet,featureGroupsComparison-method plotVenn,featureGroupsComparison-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 |
| Class for suspect screened feature groups. | 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 |
| Base features class | $,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 |
| 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 piek | findFeaturesPiek getPiekEICParams |
| 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 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 generateMSPeakLists,featureGroupsSet-method |
| Generation of transformation products (TPs) | generateTPs |
| Obtain transformation products (TPs) from compound annotation candidates | generateTPsAnnComp |
| Obtain transformation products (TPs) from formula annotation candidates | generateTPsAnnForm |
| 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 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 [ [[ |
| Automatically generate a transformation product library with formula data. | genFormulaTPLibrary |
| Background MS/MS peak detection | getBGMSMSPeaks |
| Parameters for CCS calculation | getCCSParams |
| Parameters for averaging MS peak list data | getDefAvgPListParams |
| Peak detection parameters | getDefPeakParams |
| Parameters to handle TP data with structural information | getDefTPStructParams |
| Obtains extracted ion chromatograms (EICs) | getEICs |
| Fold change calculation | getFCParams |
| Parameters for IMS matching | getIMSMatchParams |
| Parameters to specify a IMS data range | getIMSRangeParams |
| Get supported MS file formats | getMSFileFormats |
| Get supported MS file types | getMSFileTypes |
| Grouping of features | groupFeatures groupFeatures,data.frame-method groupFeatures,features-method |
| Group features using greedy algorithm | groupFeaturesGreedy groupFeaturesGreedy,features-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 |
| Identification confidence estimation | estimateIDConfidence estimateIDConfidence,compounds-method estimateIDConfidence,compoundsSet-method estimateIDConfidence,featureGroupsScreening-method estimateIDConfidence,featureGroupsScreeningSet-method estimateIDConfidence,formulas-method estimateIDConfidence,formulasSet-method genIDLevelRulesFile id-conf numericIDLevel |
| Import feature groups from files | importFeatureGroups |
| Imports feature groups from Bruker ProfileAnalysis | importFeatureGroupsBrukerPA |
| Imports feature groups from Bruker TASQ | featureGroupsBrukerTASQ featuresBrukerTASQ featuresBrukerTASQ-class importFeatureGroupsBrukerTASQ |
| Imports feature groups from enviMass | importFeatureGroupsEnviMass |
| Imports feature groups from KPIC2 | importFeatureGroupsKPIC2 |
| Import feature groups from a table | importFeatureGroupsTable |
| 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 |
| Import features from a table | importFeaturesTable |
| Imports features from XCMS (old interface) | importFeaturesXCMS |
| Imports features from XCMS (new interface) | importFeaturesXCMS3 |
| Automatically installs C3SDB | installC3SDB |
| Automatically installs TIMSCONVERT | installTIMSCONVERT |
| Conversion to KPIC2 objects | getPICSet getPICSet,features-method getPICSet,featuresKPIC2-method kpic2-conv |
| Launch EIC/EIM GUI | launchEICGUI launchEICGUI,featureGroups-method launchEICGUI,features-method |
| Default limits and tolerances | defaultLim genLimitsFile getLimIMS limits |
| 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 |
| Initiate sets workflows | makeSet makeSet,featureGroups-method makeSet,featureGroupsSet-method makeSet,features-method makeSet,featuresSet-method |
| MS data conversion | convertMSFiles convertMSFilesBruker convertMSFilesIMSCollapse convertMSFilesOpenMS convertMSFilesPaths convertMSFilesPWiz convertMSFilesTIMSCONVERT getMSConversionFormats getMSConversionTypes MSConversion |
| Interface for HRMS and IMS-HRMS raw data | availableBackends msdata |
| 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 |
| 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 spectrumSimilarityIMS spectrumSimilarityIMS,MSPeakLists-method unset,MSPeakListsSet-method [,MSPeakLists,ANY,ANY,missing-method [,MSPeakListsSet,ANY,ANY,missing-method [[,MSPeakLists,ANY,ANY-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 |
| 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 |
| Report workflow data | genReportSettingsFile report report,featureGroups-method reporting |
| Report feature group data (legacy interface) | reportCSV reportCSV,featureGroups-method reporting-legacy reportPDF reportPDF,featureGroups-method |
| Retention order direction | retDir |
| Sets workflows | sets-workflow |
| MS spectral similarity calculation parameters | getDefSpecSimParams specSimParams |
| Target and suspect screening | screenSuspects screenSuspects,featureGroups-method screenSuspects,featureGroupsScreening-method screenSuspects,featureGroupsScreeningSet-method screenSuspects,featureGroupsSet-method suspect-screening |
| Obtain default rules for metabolic logic | TPLogicTransformations |
| 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 |
| Transformation products obtained from compound annotations | filter,transformationProductsAnnComp-method transformationProductsAnnComp transformationProductsAnnComp-class |
| Transformation products obtained from formula annotations | filter,transformationProductsAnnForm-method transformationProductsAnnForm transformationProductsAnnForm-class |
| 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 |
| 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 xcms-conv |
