All functions

checkChromatograms(<featureGroups>) newProject()

Interactive GUI utilities

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()

Class containing MS Peak Lists

generateMSPeakLists(<featureGroups>) generateMSPeakListsDA() generateMSPeakListsDAFMF() generateMSPeakListsMzR() getDefAvgPListParams()

Generation of MS Peak Lists

adduct() show(<adduct>) as.character(<adduct>)

Generic adduct class

GenFormAdducts() MetFragAdducts() as.adduct() calculateIonFormula() calculateNeutralFormula()

Adduct utilities

generateAnalysisInfo() generateAnalysisInfoFromEnviMass()

Analysis information

showDataAnalysis() setDAMethod() revertDAAnalyses() recalibrarateDAFiles() getDACalibrationError() addDAEIC() addAllDAEICs()

Bruker DataAnalysis utilities

clearCache()

Clearing of cached data

generateComponents(<featureGroups>) generateComponentsCAMERA() generateComponentsIntClust() generateComponentsNontarget() generateComponentsRAMClustR()

Grouping feature groups in components

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>)

Component class

clusters(<componentsIntClust>) cutClusters(<componentsIntClust>) clusterProperties(<componentsIntClust>) treeCut(<componentsIntClust>) treeCutDynamic(<componentsIntClust>) plotHeatMap(<componentsIntClust>) plotInt(<componentsIntClust>) plot(<componentsIntClust>,<ANY>) plotSilhouettes(<componentsIntClust>)

Components based on clustered intensity profiles.

plotGraph(<componentsNT>)

Components class for homologous series.

generateCompounds(<featureGroups>) generateCompoundsMetFrag() generateCompoundsSIRIUS() compoundScorings()

Automatic compound identification

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>)

Compound lists class

makeHCluster(<compounds>)

Hierarchical clustering of compounds

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>)

Compounds cluster class

settings(<compoundsMF>)

Compounds list class for MetFrag results.

MSFileFormats() convertMSFiles()

MS data conversion

filter(<featureGroups>) replicateGroupSubtract(<featureGroups>)

Filtering of grouped features

findFeatures() importFeatures() findFeaturesBruker() findFeaturesEnviPick() importFeaturesEnviMass() findFeaturesOpenMS() findFeaturesXCMS() importFeaturesXCMS() findFeaturesXCMS3() importFeaturesXCMS3()

Finding features

groupFeatures(<features>) importFeatureGroups() importFeatureGroupsBrukerPA() importFeatureGroupsEnviMass() groupFeaturesOpenMS() groupFeaturesXCMS() importFeatureGroupsXCMS() groupFeaturesXCMS3() importFeatureGroupsXCMS3()

Grouping of features

optimizeFeatureGrouping() generateFGroupsOptPSet() getDefFGroupsOptParamRanges() optimizeFeatureFinding() generateFeatureOptPSet() getDefFeaturesOptParamRanges()

Optimization of feature finding and grouping parameters

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>)

Base class for grouped features.

comparison(<featureGroups>) plot(<featureGroupsComparison>,<ANY>) plotVenn(<featureGroupsComparison>) plotUpSet(<featureGroupsComparison>) plotChord(<featureGroupsComparison>) consensus(<featureGroupsComparison>)

Comparing feature groups

names(<featureGroupsComparison>) length(<featureGroupsComparison>) `[`(<featureGroupsComparison>,<ANY>,<missing>,<missing>) `[[`(<featureGroupsComparison>,<ANY>,<missing>) `$`(<featureGroupsComparison>)

Feature groups comparison class

screenInfo(<featureGroupsScreening>) show(<featureGroupsScreening>) `[`(<featureGroupsScreening>,<ANY>,<ANY>,<missing>) as.data.table(<featureGroupsScreening>) annotateSuspects(<featureGroupsScreening>) filter(<featureGroupsScreening>)

Class for suspect screened feature groups.

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>)

Base features class

generateFormulas(<featureGroups>) generateFormulasDA() generateFormulasGenForm() generateFormulasSIRIUS() formulaScorings()

Automatic chemical formula generation

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>)

Formula lists class

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()

Miscellaneous generics

algorithm(<optimizationResult>) length(<optimizationResult>) lengths(<optimizationResult>) show(<optimizationResult>) plot(<optimizationResult>,<ANY>) optimizedParameters(<optimizationResult>) optimizedObject(<optimizationResult>) scores(<optimizationResult>) experimentInfo(<optimizationResult>)

Class containing optimization results.

patRoon-package

Workflow solutions for mass-spectrometry based non-target analysis.

printPackageOpts()

Prints all the package options of patRoon and their currently set values.

reportCSV(<featureGroups>) reportPDF(<featureGroups>) reportHTML(<featureGroups>)

Report feature group data

screenSuspects(<featureGroups>) numericIDLevel() genIDLevelRulesFile() importFeatureGroupsBrukerTASQ()

Target and suspect screening

verifyDependencies()

Verifies if all dependencies are installed properly and instructs the user if this is not the case.

withOpt()

Temporarily changes package options

algorithm(<workflowStep>) as.data.table(<workflowStep>) as.data.frame(<workflowStep>) show(<workflowStep>)

(Virtual) Base class for all workflow objects.

getXCMSSet() getXCMSnExp()

Conversion to XCMS objects