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checkChromatograms(<featureGroups>) newProject()
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Interactive GUI utilities |
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peakLists(<MSPeakLists>) averagedPeakLists(<MSPeakLists>) analyses(<MSPeakLists>) groupNames(<MSPeakLists>) length(<MSPeakLists>) show(<MSPeakLists>) `[`(<MSPeakLists>,<ANY>,<ANY>,<missing>) `[[`(<MSPeakLists>,<ANY>,<ANY>) `$`(<MSPeakLists>) as.data.table(<MSPeakLists>) filter(<MSPeakLists>) plotSpectrum(<MSPeakLists>) getDefIsolatePrecParams()
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Class containing MS Peak Lists |
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generateMSPeakLists(<featureGroups>) generateMSPeakListsDA() generateMSPeakListsDAFMF() generateMSPeakListsMzR() getDefAvgPListParams()
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Generation of MS Peak Lists |
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adduct() show(<adduct>) as.character(<adduct>)
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Generic adduct class |
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GenFormAdducts() MetFragAdducts() as.adduct() calculateIonFormula() calculateNeutralFormula()
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Adduct utilities |
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generateAnalysisInfo() generateAnalysisInfoFromEnviMass()
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Analysis information |
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showDataAnalysis() setDAMethod() revertDAAnalyses() recalibrarateDAFiles() getDACalibrationError() addDAEIC() addAllDAEICs()
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Bruker DataAnalysis utilities |
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clearCache()
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Clearing of cached data |
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generateComponents(<featureGroups>) generateComponentsCAMERA() generateComponentsIntClust() generateComponentsNontarget() generateComponentsRAMClustR()
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Grouping feature groups in components |
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componentTable(<components>) componentInfo(<components>) groupNames(<components>) length(<components>) names(<components>) show(<components>) `[`(<components>,<ANY>,<ANY>,<missing>) `[[`(<components>,<ANY>,<ANY>) `$`(<components>) as.data.table(<components>) filter(<components>) findFGroup(<components>) plotSpectrum(<components>) plotChroms(<components>) consensus(<components>)
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Component class |
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clusters(<componentsIntClust>) cutClusters(<componentsIntClust>) clusterProperties(<componentsIntClust>) treeCut(<componentsIntClust>) treeCutDynamic(<componentsIntClust>) plotHeatMap(<componentsIntClust>) plotInt(<componentsIntClust>) plot(<componentsIntClust>,<ANY>) plotSilhouettes(<componentsIntClust>)
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Components based on clustered intensity profiles. |
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plotGraph(<componentsNT>)
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Components class for homologous series. |
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generateCompounds(<featureGroups>) generateCompoundsMetFrag() generateCompoundsSIRIUS() compoundScorings()
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Automatic compound identification |
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compoundTable(<compounds>) algorithm(<compounds>) groupNames(<compounds>) length(<compounds>) show(<compounds>) `[`(<compounds>,<ANY>,<missing>,<missing>) `[[`(<compounds>,<ANY>,<missing>) `$`(<compounds>) as.data.table(<compounds>) identifiers(<compounds>) filter(<compounds>) addFormulaScoring(<compounds>) getMCS(<compounds>) plotStructure(<compounds>) plotScores(<compounds>) annotatedPeakList(<compounds>) plotSpectrum(<compounds>) plotVenn(<compounds>) plotUpSet(<compounds>) consensus(<compounds>)
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Compound lists class |
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makeHCluster(<compounds>)
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Hierarchical clustering of compounds |
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clusters(<compoundsCluster>) cutClusters(<compoundsCluster>) clusterProperties(<compoundsCluster>) groupNames(<compoundsCluster>) length(<compoundsCluster>) lengths(<compoundsCluster>) show(<compoundsCluster>) `[`(<compoundsCluster>,<ANY>,<missing>,<missing>) treeCut(<compoundsCluster>) treeCutDynamic(<compoundsCluster>) plot(<compoundsCluster>,<ANY>) getMCS(<compoundsCluster>) plotStructure(<compoundsCluster>) plotSilhouettes(<compoundsCluster>)
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Compounds cluster class |
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settings(<compoundsMF>)
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Compounds list class for MetFrag results. |
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MSFileFormats() convertMSFiles()
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MS data conversion |
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filter(<featureGroups>) replicateGroupSubtract(<featureGroups>)
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Filtering of grouped features |
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findFeatures() importFeatures() findFeaturesBruker() findFeaturesEnviPick() importFeaturesEnviMass() findFeaturesOpenMS() findFeaturesXCMS() importFeaturesXCMS() findFeaturesXCMS3() importFeaturesXCMS3()
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Finding features |
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groupFeatures(<features>) importFeatureGroups() importFeatureGroupsBrukerPA() importFeatureGroupsEnviMass() groupFeaturesOpenMS() groupFeaturesXCMS() importFeatureGroupsXCMS() groupFeaturesXCMS3() importFeatureGroupsXCMS3()
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Grouping of features |
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optimizeFeatureGrouping() generateFGroupsOptPSet() getDefFGroupsOptParamRanges() optimizeFeatureFinding() generateFeatureOptPSet() getDefFeaturesOptParamRanges()
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Optimization of feature finding and grouping parameters |
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names(<featureGroups>) analyses(<featureGroups>) replicateGroups(<featureGroups>) groupNames(<featureGroups>) length(<featureGroups>) show(<featureGroups>) groupTable(<featureGroups>) analysisInfo(<featureGroups>) groupInfo(<featureGroups>) featureTable(<featureGroups>) getFeatures(<featureGroups>) groupFeatIndex(<featureGroups>) `[`(<featureGroups>,<ANY>,<ANY>,<missing>) `[[`(<featureGroups>,<ANY>,<ANY>) `$`(<featureGroups>) export(<featureGroups>) as.data.table(<featureGroups>) plot(<featureGroups>,<ANY>) plotInt(<featureGroups>) plotChord(<featureGroups>) plotChroms(<featureGroups>) plotVenn(<featureGroups>) plotUpSet(<featureGroups>) unique(<featureGroups>) overlap(<featureGroups>)
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Base class for grouped features. |
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comparison(<featureGroups>) plot(<featureGroupsComparison>,<ANY>) plotVenn(<featureGroupsComparison>) plotUpSet(<featureGroupsComparison>) plotChord(<featureGroupsComparison>) consensus(<featureGroupsComparison>)
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Comparing feature groups |
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names(<featureGroupsComparison>) length(<featureGroupsComparison>) `[`(<featureGroupsComparison>,<ANY>,<missing>,<missing>) `[[`(<featureGroupsComparison>,<ANY>,<missing>) `$`(<featureGroupsComparison>)
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Feature groups comparison class |
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screenInfo(<featureGroupsScreening>) show(<featureGroupsScreening>) `[`(<featureGroupsScreening>,<ANY>,<ANY>,<missing>) as.data.table(<featureGroupsScreening>) annotateSuspects(<featureGroupsScreening>) filter(<featureGroupsScreening>)
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Class for suspect screened feature groups. |
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length(<features>) show(<features>) featureTable(<features>) analysisInfo(<features>) analyses(<features>) replicateGroups(<features>) as.data.table(<features>) filter(<features>) `[`(<features>,<ANY>,<missing>,<missing>) `[[`(<features>,<ANY>,<missing>) `$`(<features>) `[`(<featuresXCMS>,<ANY>,<missing>,<missing>) filter(<featuresXCMS>) `[`(<featuresXCMS3>,<ANY>,<missing>,<missing>) filter(<featuresXCMS3>)
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Base features class |
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generateFormulas(<featureGroups>) generateFormulasDA() generateFormulasGenForm() generateFormulasSIRIUS() formulaScorings()
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Automatic chemical formula generation |
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formulaTable(<formulas>) algorithm(<formulas>) analyses(<formulas>) groupNames(<formulas>) length(<formulas>) show(<formulas>) `[`(<formulas>,<ANY>,<missing>,<missing>) `[[`(<formulas>,<ANY>,<ANY>) `$`(<formulas>) as.data.table(<formulas>) filter(<formulas>) annotatedPeakList(<formulas>) plotScores(<formulas>) plotSpectrum(<formulas>) plotVenn(<formulas>) plotUpSet(<formulas>) consensus(<formulas>)
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Formula lists class |
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algorithm() analysisInfo() analyses() annotatedPeakList() clusterProperties() clusters() cutClusters() consensus() featureTable() filter() getFeatures() getMCS() groupNames() plotChord() plotChroms() plotInt() plotScores() plotSilhouettes() plotSpectrum() plotStructure() plotVenn() plotUpSet() replicateGroups() treeCut() treeCutDynamic()
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Miscellaneous generics |
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algorithm(<optimizationResult>) length(<optimizationResult>) lengths(<optimizationResult>) show(<optimizationResult>) plot(<optimizationResult>,<ANY>) optimizedParameters(<optimizationResult>) optimizedObject(<optimizationResult>) scores(<optimizationResult>) experimentInfo(<optimizationResult>)
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Class containing optimization results. |
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patRoon-package
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Workflow solutions for mass-spectrometry based non-target analysis. |
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printPackageOpts()
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Prints all the package options of patRoon and their currently set values. |
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reportCSV(<featureGroups>) reportPDF(<featureGroups>) reportHTML(<featureGroups>)
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Report feature group data |
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screenSuspects(<featureGroups>) numericIDLevel() genIDLevelRulesFile() importFeatureGroupsBrukerTASQ()
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Target and suspect screening |
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verifyDependencies()
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Verifies if all dependencies are installed properly and instructs the user if
this is not the case. |
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withOpt()
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Temporarily changes package options |
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algorithm(<workflowStep>) as.data.table(<workflowStep>) as.data.frame(<workflowStep>) show(<workflowStep>)
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(Virtual) Base class for all workflow objects. |
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getXCMSSet() getXCMSnExp()
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Conversion to XCMS objects |