Man pages for rickhelmus/patRoon
Workflows for Mass-Spectrometry Based Non-Target Analysis
| adduct-class | Generic adduct class |
| adduct-utils | Adduct utilities |
| analysisinfo-dataframe | AnalysisInfo data.frame methods |
| analysis-information | Properties of sample analyses |
| bruker-utils | Bruker DataAnalysis utilities |
| caching | Utilities for caching of workflow data. |
| check-GUI | Interactive GUI utilities to check workflow data |
| components-class | Component class |
| componentsClust-class | Base class for components that are based on hierarchical... |
| componentsIntClust-class | Components based on clustered intensity profiles. |
| componentsNT-class | Components class for homologous series. |
| componentsSpecClust-class | Components based on MS/MS similarity. |
| componentsTPs-class | Components based on parent and transformation product (TP)... |
| compounds-class | Compound annotations class |
| compounds-cluster | Hierarchical clustering of compounds |
| compoundsCluster-class | Compounds cluster class |
| compoundScorings | Scorings terms for compound candidates |
| compoundsMF-class | Compounds list class for MetFrag results. |
| compoundsSIRIUS-class | Compounds class for SIRIUS results. |
| COMStop | Internal fix for 'RDCOMClient', ignore. |
| convertMSFiles | MS data conversion |
| createCOMReference | Internal fix for 'RDCOMClient', ignore. |
| defaultOpenMSAdducts | Default adducts for OpenMS componentization |
| EICParams | Extracted Ion Chromatogram parameters |
| executeMultiProcess | Simultaneous execution of system commands. |
| featureAnnotations-class | Base feature annotations class |
| feature-filtering | Filtering of grouped features |
| featureGroups-class | Base class for grouped features. |
| featureGroups-compare | Comparing feature groups |
| featureGroupsComparison-class | Feature groups comparison class |
| featureGroupsScreening-class | Class for suspect screened feature groups. |
| feature-optimization | Optimization of feature finding and grouping parameters |
| feature-plotting | Plotting of grouped features |
| featureQualityNames | Returns chromatographic peak quality and score names for... |
| features-class | 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 |
| findFeaturesSAFD | Find features using SAFD |
| findFeaturesSIRIUS | Find features using SIRIUS |
| findFeaturesXCMS | Find features using XCMS (old interface) |
| findFeaturesXCMS3 | Find features using XCMS (new interface) |
| formulas-class | Formula annotations class |
| formulaScorings | Scorings terms for formula candidates |
| formulasSIRIUS-class | Formulas class for SIRIUS results. |
| 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 |
| 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 |
| generateFormulasDA | Generate formula with Bruker DataAnalysis |
| generateFormulasGenForm | Generate formula with GenForm |
| generateFormulasSIRIUS | Generate formula with SIRIUS |
| generateMSPeakLists | Generation of MS Peak Lists |
| generateMSPeakListsDA | Generate peak lists with Bruker DataAnalysis |
| generateMSPeakListsDAFMF | Generate peak lists with Bruker DataAnalysis from bruker... |
| generateMSPeakListsMzR | Generate peak lists with mzR |
| generateTPs | Generation of transformation products (TPs) |
| generateTPsBioTransformer | Obtain transformation products (TPs) with BioTransformer |
| generateTPsCTS | Obtain transformation products (TPs) with Chemical... |
| generateTPsLibrary | Obtain transformation products (TPs) from a library |
| generateTPsLibraryFormula | Obtain transformation products (TPs) from a library with... |
| generateTPsLogic | Obtain transformation products (TPs) with metabolic logic |
| generics | Miscellaneous generics |
| genFormulaTPLibrary | Automatically generate a transformation product library with... |
| getDefAvgPListParams | Parameters for averaging MS peak list data |
| getEICs | Obtains extracted ion chromatograms (EICs) |
| getFCParams | Fold change calculation |
| getSIRIUSToken | Obtains a SIRIUS refresh token |
| groupFeatures | Grouping of features |
| 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) |
| 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 |
| 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 |
| importFeaturesXCMS | Imports features from XCMS (old interface) |
| importFeaturesXCMS3 | Imports features from XCMS (new interface) |
| kpic2-conv | Conversion to KPIC2 objects |
| loadMSLibrary | Loading of MS library data |
| loadMSLibraryMoNAJSON | Load MS library data from MassBank of North America (MoNA) |
| loadMSLibraryMSP | Load MS library data from MSP files |
| makeSet | Initiate sets workflows |
| MSLibrary-class | Class to store data from a loaded MS library |
| MSPeakLists-class | Class containing MS Peak Lists |
| newProject | Easily create new 'patRoon' projects |
| optimizationResult-class | Class containing optimization results. |
| patRoon-defunct | Defunct functions. |
| patRoon-deprecated | Deprecated and renamed functions. |
| patRoon-package | Workflow solutions for mass-spectrometry based non-target... |
| pred-aggr-params | Parameters to aggregate concentrations/toxicity values... |
| pred-quant | Functionality to predict quantitative data |
| pred-tox | Functionality to predict toxicities |
| printPackageOpts | Prints all the package options of 'patRoon' and their... |
| reporting | Report workflow data |
| reporting-legacy | Report feature group data (legacy interface) |
| sets-workflow | Sets workflows |
| specSimParams | MS spectral similarity calculation parameters |
| suspect-screening | Target and suspect screening |
| transformationProducts-class | Base transformation products (TP) class |
| transformationProductsFormula-class | Base transformation products (TP) class with formula... |
| transformationProductsStructure-class | Base transformation products (TP) class with structure... |
| verifyDependencies | Verifies if all dependencies are installed properly and... |
| withOpt | Temporarily changes package options |
| workflowStep-class | (Virtual) Base class for all workflow objects. |
| workflowStepSet-class | (Virtual) base class for sets related workflow objects |
| xcms-conv | Conversion to XCMS objects |
