Package index • patRoon

All functions

C3SDBAdducts(): Returns the adducts supported by C3SDB
convertMobilityToCCS() convertCCSToMobility(): Conversion between mobility and CCS
getDefEICParams() getDefEIMParams(): Extracted Ion Chromatogram and Mobilogram parameters
getMSConversionTypes() getMSConversionFormats() convertMSFilesPWiz() convertMSFilesOpenMS() convertMSFilesBruker() convertMSFilesIMSCollapse() convertMSFilesTIMSCONVERT() convertMSFilesPaths() convertMSFiles(): MS data conversion
records() spectra() length(<MSLibrary>) names(<MSLibrary>) show(<MSLibrary>) `[`(<MSLibrary>,<ANY>,<missing>,<missing>) `[[`(<MSLibrary>,<ANY>,<missing>) `$`(<MSLibrary>) as.data.table(<MSLibrary>) delete(<MSLibrary>) filter(<MSLibrary>) convertToSuspects(<MSLibrary>) export(<MSLibrary>) merge(<MSLibrary>,<MSLibrary>): Class to store data from a loaded MS library
peakLists() averagedPeakLists() spectrumSimilarity() spectrumSimilarityIMS() analyses(<MSPeakLists>) groupNames(<MSPeakLists>) length(<MSPeakLists>) show(<MSPeakLists>) `[`(<MSPeakLists>,<ANY>,<ANY>,<missing>) `[[`(<MSPeakLists>,<ANY>,<ANY>) `$`(<MSPeakLists>) as.data.table(<MSPeakLists>) delete(<MSPeakLists>) filter(<MSPeakLists>) plotSpectrum(<MSPeakLists>) analysisInfo(<MSPeakListsSet>) show(<MSPeakListsSet>) `[`(<MSPeakListsSet>,<ANY>,<ANY>,<missing>) as.data.table(<MSPeakListsSet>) delete(<MSPeakListsSet>) filter(<MSPeakListsSet>) plotSpectrum(<MSPeakListsSet>) unset(<MSPeakListsSet>) getDefIsolatePrecParams(): Class containing MS Peak Lists
TPLogicTransformations(): Obtain default rules for metabolic logic
adduct() show(<adduct>) as.character(<adduct>): Generic adduct class
GenFormAdducts() MetFragAdducts() as.adduct() calculateIonFormula() calculateNeutralFormula(): Adduct utilities
generateAnalysisInfo() generateAnalysisInfoFromEnviMass(): Properties of sample analyses
getTICs(<data.frame>) getBPCs(<data.frame>) plotTICs(<data.frame>) plotBPCs(<data.frame>) plotTICs(<data.table>) plotBPCs(<data.table>): AnalysisInfo data.frame methods
assignMobilities(<compounds>) assignMobilities(<compoundsSet>): Assign IMS data to a compounds object.
assignMobilities(<featureGroups>) assignMobilities(<featureGroupsSet>) assignMobilities(<featureGroupsScreening>) assignMobilities(<featureGroupsScreeningSet>): Assign Ion Mobility and CCS values to features
assignMobilities(<data.table>) assignMobilities(<data.frame>): Assign IMS data to suspects
showDataAnalysis() setDAMethod() revertDAAnalyses() recalibrarateDAFiles() getDACalibrationError() addDAEIC() addAllDAEICs(): Bruker DataAnalysis utilities
makeHash() makeFileHash() loadCacheData() saveCacheData() clearCache(): Utilities for caching of workflow data.
checkFeatures() checkComponents() importCheckFeaturesSession() getMCTrainData() predictCheckFeaturesSession(): Interactive GUI utilities to check workflow data
cluster-params: Clustering parameters
componentTable() componentInfo() findFGroup() expandForIMS() groupNames(<components>) length(<components>) names(<components>) show(<components>) `[`(<components>,<ANY>,<ANY>,<missing>) `[[`(<components>,<ANY>,<ANY>) `$`(<components>) delete(<components>) as.data.table(<components>) filter(<components>) plotSpectrum(<components>) plotChroms(<components>) consensus(<components>) show(<componentsFeatures>) show(<componentsSet>) `[`(<componentsSet>,<ANY>,<ANY>,<missing>) filter(<componentsSet>) delete(<componentsSet>) consensus(<componentsSet>) unset(<componentsSet>): Component class
delete(<componentsClust>) clusters(<componentsClust>) cutClusters(<componentsClust>) clusterProperties(<componentsClust>) treeCut(<componentsClust>) treeCutDynamic(<componentsClust>) plot(<componentsClust>,<missing>) plotSilhouettes(<componentsClust>): Base class for components that are based on hierarchical clustered data.
plotHeatMap() plotInt(<componentsIntClust>): Components based on clustered intensity profiles.
plotGraph(<componentsNT>) plotGraph(<componentsNTSet>) unset(<componentsNTSet>): Components class for homologous series.
plotGraph(<componentsNet>) plotGraph(<componentsNetSet>) unset(<componentsNetSet>): Components class for network-based componentization.
componentsSpecClust-class componentsSpecClust: Components based on MS/MS similarity.
as.data.table(<componentsTPs>) filter(<componentsTPs>) plotGraph(<componentsTPs>): Components based on parent and transformation product (TP) linkage.
compoundScorings(): Scorings terms for compound candidates
addFormulaScoring() defaultExclNormScores(<compounds>) show(<compounds>) identifiers(<compounds>) filter(<compounds>) getMCS(<compounds>) plotStructure(<compounds>) plotScores(<compounds>) annotatedPeakList(<compounds>) plotSpectrum(<compounds>) consensus(<compounds>) show(<compoundsSet>) delete(<compoundsSet>) `[`(<compoundsSet>,<ANY>,<missing>,<missing>) filter(<compoundsSet>) plotSpectrum(<compoundsSet>) annotatedPeakList(<compoundsSet>) consensus(<compoundsSet>) unset(<compoundsSet>) unset(<compoundsConsensusSet>) delete(<compoundsSIRIUS>): Compound annotations class
makeHCluster(): 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>,<missing>) getMCS(<compoundsCluster>) plotStructure(<compoundsCluster>) plotSilhouettes(<compoundsCluster>): Compounds cluster class
settings(): Compounds list class for MetFrag results.
compoundsSIRIUS-class compoundsSIRIUS: Compounds class for SIRIUS results.
defaultOpenMSAdducts(): Default adducts for OpenMS componentization
replicateSubtract() filter(<featureGroups>) filter(<featureGroupsSet>): Filtering of grouped features
optimizeFeatureGrouping() generateFGroupsOptPSet() getDefFGroupsOptParamRanges() optimizeFeatureFinding() generateFeatureOptPSet() getDefFeaturesOptParamRanges(): Optimization of feature finding and grouping parameters
plotMobilograms() plot(<featureGroups>,<missing>) plotInt(<featureGroups>) plotChord(<featureGroups>) plotChroms(<featureGroups>) plotChroms3D(<featureGroups>) plotChroms3D(<featureGroupsSet>) plotVenn(<featureGroups>) plotUpSet(<featureGroups>) plotVolcano(<featureGroups>) plotGraph(<featureGroups>) plotGraph(<featureGroupsSet>) plotTICs(<featureGroups>) plotBPCs(<featureGroups>): Plotting of grouped features
featureQualities() featureGroupQualities() featureQualityNames(): Feature quality definitions and utilities
as.data.table(<featureGroups>) as.data.table(<featureGroupsScreening>) as.data.table(<featureGroupsScreeningSet>): Feature group to table conversion
annotations(<featureAnnotations>) groupNames(<featureAnnotations>) length(<featureAnnotations>) `[`(<featureAnnotations>,<ANY>,<missing>,<missing>) `[[`(<featureAnnotations>,<ANY>,<missing>) `$`(<featureAnnotations>) as.data.table(<featureAnnotations>) delete(<featureAnnotations>) filter(<featureAnnotations>) plotVenn(<featureAnnotations>) plotUpSet(<featureAnnotations>): Base feature annotations class
groupTable() groupFeatIndex() groupInfo() unique() overlap() selectIons() groupQualities() groupScores() internalStandards() internalStandardAssignments() normInts() concentrations() toxicities() updateGroups() names(<featureGroups>) analyses(<featureGroups>) replicates(<featureGroups>) groupNames(<featureGroups>) length(<featureGroups>) hasIMS(<featureGroups>) fromIMS(<featureGroups>) show(<featureGroups>) analysisInfo(<featureGroups>) `analysisInfo<-`(<featureGroups>) featureTable(<featureGroups>) getFeatures(<featureGroups>) getFeatureQualityNames(<featureGroups>) annotations(<featureGroups>) adducts(<featureGroups>) `adducts<-`(<featureGroups>) `[`(<featureGroups>,<ANY>,<ANY>,<missing>) `[[`(<featureGroups>,<ANY>,<ANY>) `$`(<featureGroups>) delete(<featureGroups>) export(<featureGroups>) calculatePeakQualities(<featureGroups>) getTICs(<featureGroups>) getBPCs(<featureGroups>) sets(<featureGroupsSet>) adducts(<featureGroupsSet>) `adducts<-`(<featureGroupsSet>) delete(<featureGroupsSet>) show(<featureGroupsSet>) featureTable(<featureGroupsSet>) `[`(<featureGroupsSet>,<ANY>,<ANY>,<missing>) export(<featureGroupsSet>) unset(<featureGroupsSet>) delete(<featureGroupsKPIC2>) `analysisInfo<-`(<featureGroupsXCMS>) delete(<featureGroupsXCMS>) delete(<featureGroupsXCMS3>): Base class for grouped features.
comparison() hasIMS(<featureGroupsComparison>) plot(<featureGroupsComparison>,<missing>) plotVenn(<featureGroupsComparison>) plotUpSet(<featureGroupsComparison>) plotChord(<featureGroupsComparison>) consensus(<featureGroupsComparison>) consensus(<featureGroupsComparisonSet>): Comparing feature groups
names(<featureGroupsComparison>) length(<featureGroupsComparison>) `[`(<featureGroupsComparison>,<ANY>,<missing>,<missing>) `[[`(<featureGroupsComparison>,<ANY>,<missing>) `$`(<featureGroupsComparison>): Feature groups comparison class
screenInfo() show(<featureGroupsScreening>) `[`(<featureGroupsScreening>,<ANY>,<ANY>,<missing>) delete(<featureGroupsScreening>) filter(<featureGroupsScreening>) show(<featureGroupsScreeningSet>) `[`(<featureGroupsScreeningSet>,<ANY>,<ANY>,<missing>) delete(<featureGroupsScreeningSet>) filter(<featureGroupsScreeningSet>) unset(<featureGroupsScreeningSet>): Class for suspect screened feature groups.
length(<features>) show(<features>) featureTable(<features>) analysisInfo(<features>) getFeatureQualityNames(<features>) `analysisInfo<-`(<features>) analyses(<features>) replicates(<features>) hasIMS(<features>) fromIMS(<features>) as.data.table(<features>) filter(<features>) `[`(<features>,<ANY>,<missing>,<missing>) `[[`(<features>,<ANY>,<missing>) `$`(<features>) delete(<features>) calculatePeakQualities(<features>) getTICs(<features>) getBPCs(<features>) plotTICs(<features>) plotBPCs(<features>) sets(<featuresSet>) show(<featuresSet>) as.data.table(<featuresSet>) `[`(<featuresSet>,<ANY>,<missing>,<missing>) filter(<featuresSet>) unset(<featuresSet>) delete(<featuresKPIC2>) delete(<featuresPiek>) `analysisInfo<-`(<featuresXCMS>) delete(<featuresXCMS>) delete(<featuresXCMS3>): Base features class
findFeatures(): Finding features
findFeaturesBruker(): Find features using Bruker DataAnalysis
findFeaturesEnviPick(): Find features using enviPick
findFeaturesKPIC2(): Find features using KPIC2
findFeaturesOpenMS(): Find features using OpenMS
findFeaturesPiek() getPiekEICParams(): Find features using piek
findFeaturesSAFD(): Find features using SAFD
findFeaturesSIRIUS(): Find features using SIRIUS
findFeaturesXCMS(): Find features using XCMS (old interface)
findFeaturesXCMS3(): Find features using XCMS (new interface)
formulaScorings(): Scorings terms for formula candidates
annotations(<formulas>) analyses(<formulas>) defaultExclNormScores(<formulas>) show(<formulas>) `[[`(<formulas>,<ANY>,<ANY>) delete(<formulas>) as.data.table(<formulas>) annotatedPeakList(<formulas>) plotSpectrum(<formulas>) plotScores(<formulas>) consensus(<formulas>) show(<formulasSet>) delete(<formulasSet>) `[`(<formulasSet>,<ANY>,<missing>,<missing>) filter(<formulasSet>) plotSpectrum(<formulasSet>) annotatedPeakList(<formulasSet>) consensus(<formulasSet>) unset(<formulasSet>) unset(<formulasConsensusSet>) delete(<formulasSIRIUS>): Formula annotations class
formulasSIRIUS-class formulasSIRIUS: Formulas class for SIRIUS results.
genFormulaTPLibrary(): Automatically generate a transformation product library with formula data.
generateComponents(): Grouping feature groups in components
generateComponentsCAMERA(): Componentization of adducts, isotopes etc. with CAMERA
generateComponentsCliqueMS(): Componentization of adducts, isotopes etc. with cliqueMS
generateComponentsIntClust(): Generate components based on intensity profiles
generateComponentsNet(): Network-based componentization
generateComponentsNontarget(): Componentization of homologous series with nontarget
generateComponentsOpenMS(): Componentization of adducts, isotopes etc. with OpenMS
generateComponentsRAMClustR(): Componentization of adducts, isotopes etc. with RAMClustR
generateComponentsSpecClust(): Generate components based on MS/MS similarity
generateComponentsTPs(): Generate components of transformation products
generateCompounds(): Automatic compound annotation
generateCompoundsLibrary(): Compound annotation with an MS library
generateCompoundsMetFrag(): Compound annotation with MetFrag
generateCompoundsSIRIUS(): Compound annotation with SIRIUS
generateFormulas(): Automatic chemical formula generation
generateFormulasGenForm(): Generate formula with GenForm
generateFormulasSIRIUS(): Generate formula with SIRIUS
generateMSPeakLists(): Generation of MS Peak Lists
generateTPs(): Generation of transformation products (TPs)
generateTPsAnnComp(): Obtain transformation products (TPs) from compound annotation candidates
generateTPsAnnForm(): Obtain transformation products (TPs) from formula annotation candidates
generateTPsBioTransformer(): Obtain transformation products (TPs) with BioTransformer
generateTPsCTS(): Obtain transformation products (TPs) with Chemical Transformation Simulator (CTS)
generateTPsLibrary(): Obtain transformation products (TPs) from a library
generateTPsLibraryFormula(): Obtain transformation products (TPs) from a library with formula data
generateTPsLogic(): Obtain transformation products (TPs) with metabolic logic
adducts() `adducts<-`() algorithm() analysisInfo() `analysisInfo<-`() analyses() annotatedPeakList() annotations() assignMobilities() calculatePeakQualities() clusterProperties() clusters() consensus() convertToMFDB() convertToSuspects() cutClusters() defaultExclNormScores() export() featureTable() filter() fromIMS() getBPCs() getFeatures() getFeatureQualityNames() getMCS() getTICs() groupNames() hasIMS() plotBPCs() plotChord() plotChroms() plotChroms3D() plotGraph() plotInt() plotScores() plotSilhouettes() plotSpectrum() plotStructure() plotTICs() plotVenn() plotUpSet() predictRespFactors() predictTox() delete() plotVolcano() replicates() setObjects() sets() treeCut() treeCutDynamic() unset(): Miscellaneous generics
getBGMSMSPeaks(): Background MS/MS peak detection
getCCSParams(): Parameters for CCS calculation
getDefAvgPListParams(): Parameters for averaging MS peak list data
getDefPeakParams(): Peak detection parameters
getDefTPStructParams(): Parameters to handle TP data with structural information
getEICs(): Obtains extracted ion chromatograms (EICs)
getFCParams(): Fold change calculation
getIMSMatchParams(): Parameters for IMS matching
getIMSRangeParams(): Parameters to specify a IMS data range
getMSFileFormats(): Get supported MS file formats
getMSFileTypes(): Get supported MS file types
groupFeatures(): Grouping of features
groupFeaturesGreedy(): Group features using greedy algorithm
groupFeaturesKPIC2(): Group features using KPIC2
groupFeaturesOpenMS(): Group features using OpenMS
groupFeaturesSIRIUS(): Group features using SIRIUS
groupFeaturesXCMS(): Group features using XCMS (old interface)
groupFeaturesXCMS3(): Group features using XCMS (new interface)
estimateIDConfidence() numericIDLevel() genIDLevelRulesFile(): Identification confidence estimation
importFeatureGroups(): Import feature groups from files
importFeatureGroupsBrukerPA(): Imports feature groups from Bruker ProfileAnalysis
importFeatureGroupsBrukerTASQ(): Imports feature groups from Bruker TASQ
importFeatureGroupsEnviMass(): Imports feature groups from enviMass
importFeatureGroupsKPIC2(): Imports feature groups from KPIC2
importFeatureGroupsTable(): Import feature groups from a table
importFeatureGroupsXCMS(): Imports feature groups from XCMS (old interface)
importFeatureGroupsXCMS3(): Imports feature groups from XCMS (new interface)
importFeatures(): Import features
importFeaturesEnviMass(): Imports features from enviMass
importFeaturesKPIC2(): Imports features from KPIC2
importFeaturesTable(): Import features from a table
importFeaturesXCMS(): Imports features from XCMS (old interface)
importFeaturesXCMS3(): Imports features from XCMS (new interface)
installC3SDB(): Automatically installs C3SDB
installTIMSCONVERT(): Automatically installs TIMSCONVERT
getPICSet(): Conversion to KPIC2 objects
launchEICGUI(<data.frame>) launchEICGUI(<features>) launchEICGUI(<featureGroups>): Launch EIC/EIM GUI
defaultLim() getLimIMS() genLimitsFile(): Default limits and tolerances
loadMSLibrary(): Loading of MS library data
loadMSLibraryMSP(): Load MS library data from MSP files
loadMSLibraryMoNAJSON(): Load MS library data from MassBank of North America (MoNA)
makeSet(): Initiate sets workflows
availableBackends(): Interface for HRMS and IMS-HRMS raw data
newProject(): Easily create new patRoon projects
optimizedParameters() optimizedObject() scores() experimentInfo() algorithm(<optimizationResult>) length(<optimizationResult>) lengths(<optimizationResult>) show(<optimizationResult>) plot(<optimizationResult>,<missing>): Class containing optimization results.
patRoon patRoon-package: Workflow solutions for mass-spectrometry based non-target analysis.
getDefPredAggrParams(): Parameters to aggregate concentrations/toxicity values assigned to feature groups
calculateConcs() predictRespFactors(<compounds>) predictRespFactors(<featureGroupsScreening>) predictRespFactors(<featureGroupsScreeningSet>) predictRespFactors(<compoundsSet>) predictRespFactors(<compoundsSIRIUS>) predictRespFactors(<formulasSet>) predictRespFactors(<formulasSIRIUS>) getQuantCalibFromScreening(): Functionality to predict quantitative data
calculateTox() predictTox(<compounds>) predictTox(<featureGroupsScreening>) predictTox(<featureGroupsScreeningSet>) predictTox(<compoundsSet>) predictTox(<compoundsSIRIUS>) predictTox(<formulasSet>) predictTox(<formulasSIRIUS>): Functionality to predict toxicities
printPackageOpts(): Prints all the package options of patRoon and their currently set values.
reportCSV() reportPDF(): Report feature group data (legacy interface)
report() genReportSettingsFile(): Report workflow data
retDir: Retention order direction
sets-workflow: Sets workflows
getDefSpecSimParams(): MS spectral similarity calculation parameters
screenSuspects(): Target and suspect screening
parents() products() length(<transformationProducts>) names(<transformationProducts>) show(<transformationProducts>) `[`(<transformationProducts>,<ANY>,<missing>,<missing>) `[[`(<transformationProducts>,<ANY>,<missing>) `$`(<transformationProducts>) as.data.table(<transformationProducts>) convertToSuspects(<transformationProducts>) delete(<transformationProducts>) filter(<transformationProducts>): Base transformation products (TP) class
filter(<transformationProductsAnnComp>): Transformation products obtained from compound annotations
filter(<transformationProductsAnnForm>): Transformation products obtained from formula annotations
plotGraph(<transformationProductsFormula>): Base transformation products (TP) class with formula information
convertToMFDB(<transformationProductsStructure>) filter(<transformationProductsStructure>) plotGraph(<transformationProductsStructure>) plotVenn(<transformationProductsStructure>) plotUpSet(<transformationProductsStructure>) consensus(<transformationProductsStructure>): Base transformation products (TP) class with structure information
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.
setObjects(<workflowStepSet>) sets(<workflowStepSet>) show(<workflowStepSet>): (Virtual) base class for sets related workflow objects
getXCMSSet() getXCMSnExp(): Conversion to XCMS objects