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C3SDBAdducts()
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Returns the adducts supported by C3SDB |
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convertMobilityToCCS() convertCCSToMobility()
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Conversion between mobility and CCS |
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getDefEICParams() getDefEIMParams()
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Extracted Ion Chromatogram and Mobilogram parameters |
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getMSConversionTypes() getMSConversionFormats() convertMSFilesPWiz() convertMSFilesOpenMS() convertMSFilesBruker() convertMSFilesIMSCollapse() convertMSFilesTIMSCONVERT() convertMSFilesPaths() convertMSFiles()
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MS data conversion |
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records() spectra() length(<MSLibrary>) names(<MSLibrary>) show(<MSLibrary>) `[`(<MSLibrary>,<ANY>,<missing>,<missing>) `[[`(<MSLibrary>,<ANY>,<missing>) `$`(<MSLibrary>) as.data.table(<MSLibrary>) delete(<MSLibrary>) filter(<MSLibrary>) convertToSuspects(<MSLibrary>) export(<MSLibrary>) merge(<MSLibrary>,<MSLibrary>)
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Class to store data from a loaded MS library |
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peakLists() averagedPeakLists() spectrumSimilarity() spectrumSimilarityIMS() analyses(<MSPeakLists>) groupNames(<MSPeakLists>) length(<MSPeakLists>) show(<MSPeakLists>) `[`(<MSPeakLists>,<ANY>,<ANY>,<missing>) `[[`(<MSPeakLists>,<ANY>,<ANY>) `$`(<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()
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Class containing MS Peak Lists |
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TPLogicTransformations()
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Obtain default rules for metabolic logic |
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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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Properties of sample analyses |
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getTICs(<data.frame>) getBPCs(<data.frame>) plotTICs(<data.frame>) plotBPCs(<data.frame>) plotTICs(<data.table>) plotBPCs(<data.table>)
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AnalysisInfo data.frame methods |
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assignMobilities(<compounds>) assignMobilities(<compoundsSet>)
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Assign IMS data to a compounds object. |
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assignMobilities(<featureGroups>) assignMobilities(<featureGroupsSet>) assignMobilities(<featureGroupsScreening>) assignMobilities(<featureGroupsScreeningSet>)
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Assign Ion Mobility and CCS values to features |
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assignMobilities(<data.table>) assignMobilities(<data.frame>)
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Assign IMS data to suspects |
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showDataAnalysis() setDAMethod() revertDAAnalyses() recalibrarateDAFiles() getDACalibrationError() addDAEIC() addAllDAEICs()
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Bruker DataAnalysis utilities |
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makeHash() makeFileHash() loadCacheData() saveCacheData() clearCache()
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Utilities for caching of workflow data. |
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checkFeatures() checkComponents() importCheckFeaturesSession() getMCTrainData() predictCheckFeaturesSession()
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Interactive GUI utilities to check workflow data |
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cluster-params
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Clustering parameters |
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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>)
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Component class |
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delete(<componentsClust>) clusters(<componentsClust>) cutClusters(<componentsClust>) clusterProperties(<componentsClust>) treeCut(<componentsClust>) treeCutDynamic(<componentsClust>) plot(<componentsClust>,<missing>) plotSilhouettes(<componentsClust>)
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Base class for components that are based on hierarchical clustered data. |
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plotHeatMap() plotInt(<componentsIntClust>)
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Components based on clustered intensity profiles. |
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plotGraph(<componentsNT>) plotGraph(<componentsNTSet>) unset(<componentsNTSet>)
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Components class for homologous series. |
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componentsSpecClust-class componentsSpecClust
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Components based on MS/MS similarity. |
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as.data.table(<componentsTPs>) filter(<componentsTPs>) plotGraph(<componentsTPs>)
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Components based on parent and transformation product (TP) linkage. |
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compoundScorings()
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Scorings terms for compound candidates |
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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>)
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Compound annotations class |
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makeHCluster()
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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>,<missing>) getMCS(<compoundsCluster>) plotStructure(<compoundsCluster>) plotSilhouettes(<compoundsCluster>)
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Compounds cluster class |
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settings()
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Compounds list class for MetFrag results. |
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compoundsSIRIUS-class compoundsSIRIUS
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Compounds class for SIRIUS results. |
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defaultOpenMSAdducts()
|
Default adducts for OpenMS componentization |
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replicateSubtract() filter(<featureGroups>) filter(<featureGroupsSet>)
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Filtering of grouped 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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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>)
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Plotting of grouped features |
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featureQualities() featureGroupQualities() featureQualityNames()
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Feature quality definitions and utilities |
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as.data.table(<featureGroups>) as.data.table(<featureGroupsScreening>) as.data.table(<featureGroupsScreeningSet>)
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Feature group to table conversion |
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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>)
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Base feature annotations class |
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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>) `$`(<featureGroups>) delete(<featureGroups>) export(<featureGroups>) calculatePeakQualities(<featureGroups>) getTICs(<featureGroups>) getBPCs(<featureGroups>) sets(<featureGroupsSet>) adducts(<featureGroupsSet>) `adducts<-`(<featureGroupsSet>) delete(<featureGroupsSet>) show(<featureGroupsSet>) featureTable(<featureGroupsSet>) `[`(<featureGroupsSet>,<ANY>,<ANY>,<missing>) export(<featureGroupsSet>) unset(<featureGroupsSet>) delete(<featureGroupsKPIC2>) `analysisInfo<-`(<featureGroupsXCMS>) delete(<featureGroupsXCMS>) delete(<featureGroupsXCMS3>)
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Base class for grouped features. |
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comparison() hasIMS(<featureGroupsComparison>) plot(<featureGroupsComparison>,<missing>) plotVenn(<featureGroupsComparison>) plotUpSet(<featureGroupsComparison>) plotChord(<featureGroupsComparison>) consensus(<featureGroupsComparison>) consensus(<featureGroupsComparisonSet>)
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Comparing feature groups |
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names(<featureGroupsComparison>) length(<featureGroupsComparison>) `[`(<featureGroupsComparison>,<ANY>,<missing>,<missing>) `[[`(<featureGroupsComparison>,<ANY>,<missing>) `$`(<featureGroupsComparison>)
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Feature groups comparison class |
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screenInfo() show(<featureGroupsScreening>) `[`(<featureGroupsScreening>,<ANY>,<ANY>,<missing>) delete(<featureGroupsScreening>) filter(<featureGroupsScreening>) show(<featureGroupsScreeningSet>) `[`(<featureGroupsScreeningSet>,<ANY>,<ANY>,<missing>) delete(<featureGroupsScreeningSet>) filter(<featureGroupsScreeningSet>) unset(<featureGroupsScreeningSet>)
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Class for suspect screened feature groups. |
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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>)
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Base features class |
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findFeatures()
|
Finding features |
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findFeaturesBruker()
|
Find features using Bruker DataAnalysis |
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findFeaturesEnviPick()
|
Find features using enviPick |
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findFeaturesKPIC2()
|
Find features using KPIC2 |
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findFeaturesOpenMS()
|
Find features using OpenMS |
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findFeaturesPiek() getPiekEICParams()
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Find features using piek |
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findFeaturesSAFD()
|
Find features using SAFD |
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findFeaturesSIRIUS()
|
Find features using SIRIUS |
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findFeaturesXCMS()
|
Find features using XCMS (old interface) |
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findFeaturesXCMS3()
|
Find features using XCMS (new interface) |
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formulaScorings()
|
Scorings terms for formula candidates |
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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>)
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Formula annotations class |
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formulasSIRIUS-class formulasSIRIUS
|
Formulas class for SIRIUS results. |
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genFormulaTPLibrary()
|
Automatically generate a transformation product library with formula data. |
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generateComponents()
|
Grouping feature groups in components |
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generateComponentsCAMERA()
|
Componentization of adducts, isotopes etc. with CAMERA |
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generateComponentsCliqueMS()
|
Componentization of adducts, isotopes etc. with cliqueMS |
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generateComponentsIntClust()
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Generate components based on intensity profiles |
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generateComponentsNontarget()
|
Componentization of homologous series with nontarget |
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generateComponentsOpenMS()
|
Componentization of adducts, isotopes etc. with OpenMS |
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generateComponentsRAMClustR()
|
Componentization of adducts, isotopes etc. with RAMClustR |
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generateComponentsSpecClust()
|
Generate components based on MS/MS similarity |
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generateComponentsTPs()
|
Generate components of transformation products |
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generateCompounds()
|
Automatic compound annotation |
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generateCompoundsLibrary()
|
Compound annotation with an MS library |
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generateCompoundsMetFrag()
|
Compound annotation with MetFrag |
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generateCompoundsSIRIUS()
|
Compound annotation with SIRIUS |
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generateFormulas()
|
Automatic chemical formula generation |
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generateFormulasGenForm()
|
Generate formula with GenForm |
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generateFormulasSIRIUS()
|
Generate formula with SIRIUS |
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generateMSPeakLists()
|
Generation of MS Peak Lists |
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generateTPs()
|
Generation of transformation products (TPs) |
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generateTPsAnnComp()
|
Obtain transformation products (TPs) from compound annotation candidates |
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generateTPsAnnForm()
|
Obtain transformation products (TPs) from formula annotation candidates |
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generateTPsBioTransformer()
|
Obtain transformation products (TPs) with BioTransformer |
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generateTPsCTS()
|
Obtain transformation products (TPs) with Chemical Transformation Simulator (CTS) |
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generateTPsLibrary()
|
Obtain transformation products (TPs) from a library |
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generateTPsLibraryFormula()
|
Obtain transformation products (TPs) from a library with formula data |
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generateTPsLogic()
|
Obtain transformation products (TPs) with metabolic logic |
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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()
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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 |