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 |