rickhelmus/patRoon
Workflows for Mass-Spectrometry Based Non-Target Analysis

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Functions
1384
Source code
233
Man pages
126
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rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis
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API

API for rickhelmus/patRoon
Workflows for Mass-Spectrometry Based Non-Target Analysis

Global functions
$ Man page
$,MSLibrary-method Man page
$,MSPeakLists-method Man page
$,components-method Man page
$,featureAnnotations-method Man page
$,featureGroups-method Man page
$,featureGroupsComparison-method Man page
$,features-method Man page
$,transformationProducts-method Man page
.onAttach Source code
.onLoad Source code
BTMPFinishHandler Source code
COMStop Man page Source code
EICParams Man page
FUN Source code Source code Source code
GenFormAdducts Man page Source code
GenFormMPFinishHandler Source code
GenFormMPPrepareHandler Source code
GenFormMPTimeoutHandler Source code
MFMPErrorHandler Source code
MFMPFinishHandler Source code
MFMPPrepareHandler Source code
MFMPTimeoutHandler Source code
MSFileExtensions Source code
MSFileFormatIsDir Source code
MSFileFormats Man page Source code
MSLibrary Man page
MSLibrary-class Man page
MSPeakLists Man page
MSPeakLists-class Man page
MSPeakListsSet Man page
MSPeakListsSet-class Man page
MSPeakListsUnset Man page
MSPeakListsUnset-class Man page
MetFragAdducts Man page Source code
NAToZero Source code
NULLToZero Source code
OpenMSArgListToOpts Source code
OpenMSVersionAtLeast Source code
RUserDir Source code
ReduceWithArgs Source code
SAFDMPFinishHandler Source code
SIRFeatMPFinishHandler Source code
SIRFeatMPPrepareHandler Source code
SIRMPFinishHandler Source code
SIRMPPrepareHandler Source code
TASQImportCols Source code
XCMSFeatCols Source code
XCMSFeatTblEqual Source code
[ Man page
[,MSLibrary,ANY,missing,missing-method Man page
[,MSPeakLists,ANY,ANY,missing-method Man page
[,MSPeakListsSet,ANY,ANY,missing-method Man page
[,components,ANY,ANY,missing-method Man page
[,componentsSet,ANY,ANY,missing-method Man page
[,compoundsCluster,ANY,missing,missing-method Man page
[,compoundsSet,ANY,missing,missing-method Man page
[,featureAnnotations,ANY,missing,missing-method Man page
[,featureGroups,ANY,ANY,missing-method Man page
[,featureGroupsComparison,ANY,missing,missing-method Man page
[,featureGroupsScreening,ANY,ANY,missing-method Man page
[,featureGroupsScreeningSet,ANY,ANY,missing-method Man page
[,featureGroupsSet,ANY,ANY,missing-method Man page
[,features,ANY,missing,missing-method Man page
[,featuresSet,ANY,missing,missing-method Man page
[,formulasSet,ANY,missing,missing-method Man page
[,transformationProducts,ANY,missing,missing-method Man page
[[ Man page
[[,MSLibrary,ANY,missing-method Man page
[[,MSPeakLists,ANY,ANY-method Man page
[[,components,ANY,ANY-method Man page
[[,featureAnnotations,ANY,missing-method Man page
[[,featureGroups,ANY,ANY-method Man page
[[,featureGroupsComparison,ANY,missing-method Man page
[[,features,ANY,missing-method Man page
[[,formulas,ANY,ANY-method Man page
[[,transformationProducts,ANY,missing-method Man page
aapply Source code
addAllDAEICs Man page Source code
addCompoundScore Source code
addDAEIC Man page Source code
addElementInfoToAnnTable Source code
addFilesToOpenMSIni Source code
addFormula Source code
addFormulaScoring Man page
addFormulaScoring,compounds-method Man page
addFormulaScoring,compoundsSet-method Man page
addMiscFormulaInfo Source code
adduct Man page
adduct-class Man page
adduct-utils Man page
adducts Man page
adducts,featureGroups-method Man page
adducts,featureGroupsSet-method Man page
adducts<- Man page
adducts<-,featureGroups-method Man page
adducts<-,featureGroupsSet-method Man page
adjustReportSettings Source code
aggrVec Source code
algorithm Man page
algorithm,optimizationResult-method Man page
algorithm,workflowStep-method Man page
allArgs Source code
allSame Source code
analyses Man page
analyses,MSPeakLists-method Man page
analyses,featureGroups-method Man page
analyses,features-method Man page
analyses,formulas-method Man page
analysis-information Man page
analysisInfo Man page
analysisInfo,MSPeakListsSet-method Man page
analysisInfo,featureGroups-method Man page
analysisInfo,features-method Man page
analysisinfo-dataframe Man page
annotateSuspects Man page
annotateSuspects,featureGroupsScreening-method Man page
annotateSuspects,featureGroupsScreeningSet-method Man page
annotatedPeakList Man page
annotatedPeakList,compounds-method Man page
annotatedPeakList,compoundsSet-method Man page
annotatedPeakList,formulas-method Man page
annotatedPeakList,formulasSet-method Man page
annotations Man page
annotations,featureAnnotations-method Man page
annotations,featureGroups-method Man page
annotations,formulas-method Man page
as.adduct Man page Source code
as.character,adduct-method Man page
as.data.frame Man page
as.data.frame,workflowStep-method Man page
as.data.table Man page
as.data.table,MSLibrary-method Man page
as.data.table,MSPeakLists-method Man page
as.data.table,MSPeakListsSet-method Man page
as.data.table,components-method Man page
as.data.table,componentsTPs-method Man page
as.data.table,featureAnnotations-method Man page
as.data.table,featureGroups-method Man page
as.data.table,featureGroupsScreening-method Man page
as.data.table,featureGroupsScreeningSet-method Man page
as.data.table,features-method Man page
as.data.table,featuresSet-method Man page
as.data.table,formulas-method Man page
as.data.table,transformationProducts-method Man page
as.data.table,workflowStep-method Man page
asAdductVec Source code
assertAnalysisInfo Source code
assertAndGetMSPLSetsArgs Source code
assertAndPrepareAnaInfo Source code
assertAndPrepareQuantCalib Source code
assertAndPrepareReportSettings Source code
assertAndPrepareSuspectsSets Source code
assertAvgPListParams Source code
assertCanCreateDir Source code
assertCanCreateDirs Source code
assertCharOrFactor Source code
assertCheckSession Source code
assertConsCommonArgs Source code
assertDACloseSaveArgs Source code
assertDeleteArgAndToChr Source code
assertDynamicTreeCutArgs Source code
assertEICParams Source code
assertFCParams Source code
assertFGAsDataTableArgs Source code
assertListVal Source code
assertLogicTransformations Source code
assertMakeSetArgs Source code
assertNormalizationMethod Source code
assertOptimArgs Source code
assertPListIsolatePrecParams Source code
assertPredAggrParams Source code
assertScoreRange Source code
assertSets Source code
assertSpecSimParams Source code
assertSubsetArgAndToChr Source code
assertSuspectList Source code
assertXYLim Source code
averageFormulas Source code
averageSpectra Source code
averagedPeakLists Man page
averagedPeakLists,MSPeakLists-method Man page
babelConvert Source code
baseName Source code
binSpectra Source code
blankFilter Source code
bruker-utils Man page
bsCardBodyNoFill Source code
buildMFLandingURL Source code
caching Man page
calcSpecSimilarity Source code
calculateComponentIntensities Source code
calculateConcs Man page
calculateConcs,featureGroups-method Man page
calculateConcs,featureGroupsScreening-method Man page
calculateConcs,featureGroupsScreeningSet-method Man page
calculateConcs,featureGroupsSet-method Man page
calculateFormScoreRanges Source code
calculateIonFormula Man page Source code
calculateLogP Source code
calculateMasses Source code
calculateNeutralFormula Man page Source code
calculatePeakQualities Man page
calculatePeakQualities,featureGroups-method Man page
calculatePeakQualities,features-method Man page
calculateTox Man page
calculateTox,featureGroups-method Man page
calculateTox,featureGroupsScreening-method Man page
calculateTox,featureGroupsScreeningSet-method Man page
calculateTox,featureGroupsSet-method Man page
callAllNextMethods Source code
check-GUI Man page
checkAndGetIonization Source code
checkAndToAdduct Source code
checkAndUnSetOther Source code
checkCSVFile Source code
checkChoiceSilent Source code
checkChromatograms Man page Source code
checkComponents Man page
checkComponents,components-method Man page
checkConcUnit Source code
checkDAFMFCompounds Source code
checkDeleteArg Source code
checkExtractArg Source code
checkFeatures Man page
checkFeatures,featureGroups-method Man page
checkFeaturesFilter Source code
checkFormula Source code
checkHasNames Source code
checkPackage Source code
checkQuantEluent Source code
checkRange Source code
checkS4 Source code
checkSetLabels Source code
checkSubsetArg Source code
chromWidthFilter Source code
classifyFormula Source code
cleanFragFormulas Source code
clearCache Man page Source code
clearDAChromsAndSpecs Source code
closeCacheDB Source code
closeSaveDAFile Source code
clusterProperties Man page
clusterProperties,componentsClust-method Man page
clusterProperties,compoundsCluster-method Man page
clusters Man page
clusters,componentsClust-method Man page
clusters,compoundsCluster-method Man page
compScoreNames Source code
comparison Man page
comparison,featureGroups-method Man page
comparison,featureGroupsSet-method Man page
componentInfo Man page
componentInfo,components-method Man page
componentTable Man page
componentTable,components-method Man page
components Man page
components-class Man page
componentsCamera Man page
componentsCamera-class Man page
componentsCliqueMS Man page
componentsCliqueMS-class Man page
componentsClust Man page
componentsClust-class Man page
componentsFeatures Man page
componentsFeatures-class Man page
componentsIntClust Man page
componentsIntClust-class Man page
componentsNT Man page
componentsNT-class Man page
componentsNTSet Man page
componentsNTSet-class Man page
componentsNTUnset Man page
componentsNTUnset-class Man page
componentsOpenMS Man page
componentsOpenMS-class Man page
componentsRC Man page
componentsRC-class Man page
componentsSet Man page
componentsSet-class Man page
componentsSpecClust Man page
componentsSpecClust-class Man page
componentsTPs Man page
componentsTPs-class Man page
componentsUnset Man page
componentsUnset-class Man page
compoundScorings Man page Source code
compoundTable Man page Source code
compoundViewer Man page
compoundViewer,featureGroups,MSPeakLists,compounds-method Man page
compounds Man page
compounds-class Man page
compounds-cluster Man page
compoundsCluster Man page
compoundsCluster-class Man page
compoundsConsensus Man page
compoundsConsensus-class Man page
compoundsConsensusSet Man page
compoundsConsensusSet-class Man page
compoundsMF Man page
compoundsMF-class Man page
compoundsSIRIUS Man page
compoundsSIRIUS-class Man page
compoundsSet Man page
compoundsSet-class Man page
compoundsUnset Man page
compoundsUnset-class Man page
concentrations Man page
concentrations,featureGroups-method Man page
consensus Man page
consensus,components-method Man page
consensus,componentsSet-method Man page
consensus,compounds-method Man page
consensus,compoundsSet-method Man page
consensus,featureGroupsComparison-method Man page
consensus,featureGroupsComparisonSet-method Man page
consensus,formulas-method Man page
consensus,formulasSet-method Man page
consensus,transformationProductsStructure-method Man page
convertFGroupsToPseudoFeatures Source code
convertMSFiles Man page Source code
convertMSFilesBruker Source code
convertMSFilesOpenMS Source code
convertMSFilesPWiz Source code
convertToMFDB Man page
convertToMFDB,transformationProductsStructure-method Man page
convertToSuspects Man page
convertToSuspects,MSLibrary-method Man page
convertToSuspects,transformationProducts-method Man page
convertXCMS3GroupListToParam Source code
convertXCMS3RetAlignListToParam Source code
countCharInStr Source code
countUniqueFormulas Source code
createCOMReference Man page Source code
curTimeMS Source code
cutClusters Man page
cutClusters,componentsClust-method Man page
cutClusters,compoundsCluster-method Man page
dbWithWriteTransaction Source code
defMultiProcErrorHandler Source code
defaultExclNormScores Man page
defaultExclNormScores,compounds-method Man page
defaultExclNormScores,formulas-method Man page
defaultOpenMSAdducts Man page Source code
defaultPkgOpts Source code
delete Man page
delete,MSLibrary-method Man page
delete,MSPeakLists-method Man page
delete,MSPeakListsSet-method Man page
delete,components-method Man page
delete,componentsClust-method Man page
delete,componentsSet-method Man page
delete,compoundsSIRIUS-method Man page
delete,compoundsSet-method Man page
delete,featureAnnotations-method Man page
delete,featureGroups-method Man page
delete,featureGroupsKPIC2-method Man page
delete,featureGroupsScreening-method Man page
delete,featureGroupsScreeningSet-method Man page
delete,featureGroupsSet-method Man page
delete,featureGroupsXCMS-method Man page
delete,featureGroupsXCMS3-method Man page
delete,features-method Man page
delete,featuresKPIC2-method Man page
delete,featuresXCMS-method Man page
delete,featuresXCMS3-method Man page
delete,formulas-method Man page
delete,formulasSIRIUS-method Man page
delete,formulasSet-method Man page
delete,transformationProducts-method Man page
distSMILES Source code
doApply Source code
doConvertToMFDB Source code
doCreateProject Source code
doDynamicTreeCut Source code
doFGAsDataTable Source code
doFGroupsFilter Source code
doGenComponentsTPs Source code
doGenerateTPsLogic Source code
doGetEICs Source code
doGroupFeaturesKPIC2 Source code
doGroupFeaturesXCMS Source code
doGroupFeaturesXCMS3 Source code
doMakeFeaturesSet Source code
doProgress Source code
doReportHTML Source code
doSIRIUS Source code
doSIRIUSFGroups Source code
doScreenSuspects Source code
doScreeningShow Source code
dumpPkgOpts Source code
emptyMSPeakList Source code
emptyMol Source code
executeCommand Source code
executeFutureCmd Source code
executeMultiProcess Man page Source code
executeMultiProcessClassic Source code
executeMultiProcessFuture Source code
experimentInfo Man page
experimentInfo,optimizationResult-method Man page
export Man page
export,MSLibrary-method Man page
export,featureGroups-method Man page
export,featureGroupsSet-method Man page
exportDAFiles Man page Source code
extractPAGroupInfo Source code
f Source code Source code
featAnnSetSpecificScoreCols Source code
featGroupTabHasSusps Source code
featQualityFilter Source code
feature-filtering Man page
feature-optimization Man page
feature-plotting Man page
featureAnnotations Man page
featureAnnotations-class Man page
featureGroupQualities Source code
featureGroups Man page
featureGroups-class Man page
featureGroups-compare Man page
featureGroupsBruker Man page
featureGroupsBruker-class Man page
featureGroupsBrukerTASQ Man page
featureGroupsBrukerTASQ-class Man page
featureGroupsComparison Man page
featureGroupsComparison-class Man page
featureGroupsComparisonSet Man page
featureGroupsComparisonSet-class Man page
featureGroupsConsensus Man page
featureGroupsConsensus-class Man page
featureGroupsEnviMass Man page
featureGroupsEnviMass-class Man page
featureGroupsKPIC2 Man page
featureGroupsKPIC2-class Man page
featureGroupsOpenMS Man page
featureGroupsOpenMS-class Man page
featureGroupsSIRIUS Man page
featureGroupsSIRIUS-class Man page
featureGroupsScreening Man page
featureGroupsScreening-class Man page
featureGroupsScreeningSet Man page
featureGroupsScreeningSet-class Man page
featureGroupsSet Man page
featureGroupsSet-class Man page
featureGroupsSetScreeningUnset Man page
featureGroupsSetScreeningUnset-class Man page
featureGroupsUnset Man page
featureGroupsUnset-class Man page
featureGroupsXCMS Man page
featureGroupsXCMS-class Man page
featureGroupsXCMS3 Man page
featureGroupsXCMS3-class Man page
featureQualities Source code
featureQualityNames Man page Source code
featureTable Man page
featureTable,featureGroups-method Man page
featureTable,featureGroupsSet-method Man page
featureTable,features-method Man page
features Man page
features-class Man page
featuresBruker Man page
featuresBruker-class Man page
featuresBrukerTASQ Man page
featuresBrukerTASQ-class Man page
featuresConsensus Man page
featuresConsensus-class Man page
featuresEnviPick Man page
featuresEnviPick-class Man page
featuresFromFeatGroups Man page
featuresFromFeatGroups-class Man page
featuresKPIC2 Man page
featuresKPIC2-class Man page
featuresOpenMS Man page
featuresOpenMS-class Man page
featuresSAFD Man page
featuresSAFD-class Man page
featuresSIRIUS Man page
featuresSIRIUS-class Man page
featuresSet Man page
featuresSet-class Man page
featuresUnset Man page
featuresUnset-class Man page
featuresXCMS Man page
featuresXCMS-class Man page
featuresXCMS3 Man page
featuresXCMS3-class Man page
filter Man page
filter,MSLibrary-method Man page
filter,MSPeakLists-method Man page
filter,MSPeakListsSet-method Man page
filter,components-method Man page
filter,componentsSet-method Man page
filter,componentsTPs-method Man page
filter,compounds-method Man page
filter,compoundsSet-method Man page
filter,featureAnnotations-method Man page
filter,featureGroups-method Man page
filter,featureGroupsScreening-method Man page
filter,featureGroupsScreeningSet-method Man page
filter,featureGroupsSet-method Man page
filter,features-method Man page
filter,featuresSet-method Man page
filter,formulasSet-method Man page
filter,transformationProducts-method Man page
filter,transformationProductsStructure-method Man page
filterMSFileDirs Source code
findFGroup Man page
findFGroup,components-method Man page
findFeatures Man page Source code
findFeaturesBruker Man page Source code
findFeaturesEnviPick Man page Source code
findFeaturesKPIC2 Man page Source code
findFeaturesOpenMS Man page Source code
findFeaturesSAFD Man page
findFeaturesSIRIUS Man page Source code
findFeaturesXCMS Man page Source code
findFeaturesXCMS3 Man page Source code
findPWizPath Source code
fixOptParamRange Source code
formScoreNames Source code
formulaListToString Source code
formulaMW Source code
formulaScorings Man page Source code
formulaTable Man page Source code
formulas Man page
formulas-class Man page
formulasConsensus Man page
formulasConsensus-class Man page
formulasConsensusSet Man page
formulasConsensusSet-class Man page
formulasSIRIUS Man page
formulasSIRIUS-class Man page
formulasSet Man page
formulasSet-class Man page
formulasUnset Man page
formulasUnset-class Man page
fprintf Source code
genClustComponentInfo Source code
genClustComponents Source code
genCompClustsImgs Source code
genCompoundsTable Source code
genConcsTable Source code
genFormulaTPLibrary Man page Source code
genFormulasTable Source code
genHTMLReportPlotsChromsFeatures Source code
genHTMLReportPlotsChromsLarge Source code
genHTMLReportPlotsChromsSmall Source code
genHTMLReportPlotsComponents Source code
genHTMLReportPlotsIntPlots Source code
genHTMLReportPlotsTPs Source code
genIDLevelRulesFile Man page Source code
genISTDGraph Source code
genMSPLTable Source code
genReportSettingsFile Man page Source code
genSuspAnnTable Source code
genTPAnnSimilarities Source code
genTPSpecSimilarities Source code
genToxTable Source code
generateAnalysisInfo Man page Source code
generateAnalysisInfoFromEnviMass Man page Source code
generateComponents Man page
generateComponents,featureGroups-method Man page
generateComponentsCAMERA Man page
generateComponentsCAMERA,featureGroups-method Man page
generateComponentsCAMERA,featureGroupsSet-method Man page
generateComponentsCliqueMS Man page
generateComponentsCliqueMS,featureGroups-method Man page
generateComponentsCliqueMS,featureGroupsSet-method Man page
generateComponentsIntClust Man page
generateComponentsIntClust,featureGroups-method Man page
generateComponentsNontarget Man page
generateComponentsNontarget,featureGroups-method Man page
generateComponentsNontarget,featureGroupsSet-method Man page
generateComponentsOpenMS Man page
generateComponentsOpenMS,featureGroups-method Man page
generateComponentsOpenMS,featureGroupsSet-method Man page
generateComponentsRAMClustR Man page
generateComponentsRAMClustR,featureGroups-method Man page
generateComponentsRAMClustR,featureGroupsSet-method Man page
generateComponentsSet Source code
generateComponentsSpecClust Man page
generateComponentsSpecClust,featureGroups-method Man page
generateComponentsTPs Man page
generateComponentsTPs,featureGroups-method Man page
generateComponentsTPs,featureGroupsSet-method Man page
generateCompounds Man page
generateCompounds,featureGroups-method Man page
generateCompoundsLibrary Man page
generateCompoundsLibrary,featureGroups-method Man page
generateCompoundsLibrary,featureGroupsSet-method Man page
generateCompoundsMetFrag Man page
generateCompoundsMetFrag,featureGroups-method Man page
generateCompoundsMetFrag,featureGroupsSet-method Man page
generateCompoundsSIRIUS Man page
generateCompoundsSIRIUS,featureGroups-method Man page
generateCompoundsSIRIUS,featureGroupsSet-method Man page
generateCompoundsSet Source code
generateConsensusXML Source code
generateDAEICsForPeakLists Source code
generateDASpecsForPeakLists Source code
generateFGroupsOptPSet Man page Source code
generateFGroupsOptPSetKPIC2 Source code
generateFGroupsOptPSetOpenMS Source code
generateFGroupsOptPSetXCMS Source code
generateFGroupsOptPSetXCMS3 Source code
generateFeatureOptPSet Man page Source code
generateFeatureOptPSetEnviPick Source code
generateFeatureOptPSetKPIC2 Source code
generateFeatureOptPSetOpenMS Source code
generateFeatureOptPSetXCMS Source code
generateFeatureOptPSetXCMS3 Source code
generateFormConsensusForGroup Source code
generateFormulasDA Man page
generateFormulasDA,featureGroups-method Man page
generateFormulasDA,featureGroupsSet-method Man page
generateFormulasGenForm Man page
generateFormulasGenForm,featureGroups-method Man page
generateFormulasGenForm,featureGroupsSet-method Man page
generateFormulasSIRIUS Man page
generateFormulasSIRIUS,featureGroups-method Man page
generateFormulasSIRIUS,featureGroupsSet-method Man page
generateFormulasSet Source code
generateGroupFormulasByConsensus Source code
generateHTMLReportPlots Source code
generateMSPeakLists Man page
generateMSPeakLists,featureGroups-method Man page
generateMSPeakListsDA Man page
generateMSPeakListsDA,featureGroups-method Man page
generateMSPeakListsDA,featureGroupsSet-method Man page
generateMSPeakListsDAFMF Man page
generateMSPeakListsDAFMF,featureGroups-method Man page
generateMSPeakListsDAFMF,featureGroupsSet-method Man page
generateMSPeakListsMzR Man page
generateMSPeakListsMzR,featureGroups-method Man page
generateMSPeakListsMzR,featureGroupsSet-method Man page
generateMSPeakListsSet Source code
generateMetFragRunData Source code
generateTPs Man page Source code
generateTPsBioTransformer Man page
generateTPsCTS Man page Source code
generateTPsLibrary Man page Source code
generateTPsLibraryFormula Man page Source code
generateTPsLogic Man page
generateTPsLogic,featureGroups-method Man page
generateTPsLogic,featureGroupsSet-method Man page
generics Man page
getAllMergedConsCols Source code
getAllMethods Source code
getAllSuspCols Source code
getAndPrepareSIRIUSResFiles Source code
getArgNames Source code
getBPCs Man page Man page Man page Man page
getBPCs,data.frame-method Man page
getBPCs,featureGroups-method Man page
getBPCs,features-method Man page
getBaseBTCmd Source code
getBrewerPal Source code
getBrukerAnalysisPath Source code
getCacheFile Source code
getCacheMode Source code
getCheckUI Source code
getCompInfoList Source code
getCompInfoText Source code
getCompViewerUI Source code
getCompoundsSpecPlotTitle Source code
getDAApplication Source code
getDACalibrationError Man page Source code
getDAFeatures Source code
getDAFileIndex Source code
getDAMaxIntMZAndFWHM Source code
getDAPeakList Source code
getDefAvgPListParams Man page Source code
getDefAvgPListParamsRD Source code
getDefEICParams Man page Source code
getDefFGroupsOptParamRanges Man page Source code
getDefFGroupsOptParamRangesKPIC2 Source code
getDefFGroupsOptParamRangesOpenMS Source code
getDefFGroupsOptParamRangesXCMS Source code
getDefFGroupsOptParamRangesXCMS3 Source code
getDefFeaturesOptParamRanges Man page Source code
getDefFeaturesOptParamRangesEnviPick Source code
getDefFeaturesOptParamRangesKPIC2 Source code
getDefFeaturesOptParamRangesOpenMS Source code
getDefFeaturesOptParamRangesXCMS Source code
getDefIsolatePrecParams Man page Source code
getDefIsolatePrecParamsRD Source code
getDefPredAggrParams Man page Source code
getDefSpecSimParams Man page Source code
getDuplicatedStrings Source code
getEICs Man page Source code
getElements Source code
getEmptyDAFragInfo Source code
getEmptyGFFragInfo Source code
getExtDepPath Source code
getFCParams Man page Source code
getFGColGrpStartCols Source code
getFGColSepStyle Source code
getFGGroupDefs Source code
getFGTable Source code
getFGroupAdducts Source code
getFeatGroupColDefs Source code
getFeatIndicesFromPA Source code
getFeatIndicesFromXCMSnExp Source code
getFeatIndicesFromXS Source code
getFeatures Man page
getFeatures,featureGroups-method Man page
getFormInfoList Source code
getFormulaDiffText Source code
getFormulaFromSIRIUSResFile Source code
getGenFormBin Source code
getHTMLReportPlotPath Source code
getHeaders Source code
getHighestAbsValue Source code
getIKBlock1 Source code
getIonizationFromAnnTable Source code
getKeptXCMSPeakInds Source code
getMCS Man page
getMCS,compounds-method Man page
getMCS,compoundsCluster-method Man page
getMCTrainData Man page
getMFFragmentInfo Source code
getMS2QuantRes Source code
getMSFilePaths Source code
getMSPlotData Source code
getMaxCacheEntries Source code
getMetFragExtDB Source code
getMoleculesFromSMILES Source code
getMzMLAnalysisPath Source code
getMzMLOrMzXMLAnalysisPath Source code
getMzXMLAnalysisPath Source code
getNeutralMassFromSMILES Source code
getNewProjectUI Source code
getNewProjectWidgetTypes Source code
getOpenMSFFCommand Source code
getOpenMSMADCommand Source code
getPICSet Man page
getPICSet,features-method Man page
getPICSet,featuresKPIC2-method Man page
getQuantCalibFromScreening Man page Source code
getRCDKStructurePlot Source code
getSIRIUSCmpName Source code
getSIRIUSToken Man page Source code
getScriptCode Source code
getSiriusBin Source code
getSiriusResultPath Source code
getSpectraHeader Source code
getStrListWithMax Source code
getTICs Man page Man page Man page Man page
getTICs,data.frame-method Man page
getTICs,featureGroups-method Man page
getTICs,features-method Man page
getTPGenInputs Source code
getTPLogicTransformations Source code
getTPParents Source code
getUISettings Source code
getUISettingsPath Source code
getXCMSSet Man page
getXCMSSet,featureGroups-method Man page
getXCMSSet,featureGroupsSet-method Man page
getXCMSSet,featureGroupsXCMS-method Man page
getXCMSSet,features-method Man page
getXCMSSet,featuresSet-method Man page
getXCMSSet,featuresXCMS-method Man page
getXCMSnExp Man page
getXCMSnExp,featureGroups-method Man page
getXCMSnExp,featureGroupsSet-method Man page
getXCMSnExp,featureGroupsXCMS3-method Man page
getXCMSnExp,features-method Man page
getXCMSnExp,featuresSet-method Man page
getXCMSnExp,featuresXCMS3-method Man page
groupFeatIndex Man page
groupFeatIndex,featureGroups-method Man page
groupFeatures Man page
groupFeatures,data.frame-method Man page
groupFeatures,features-method Man page
groupFeatures,featuresSet-method Man page
groupFeaturesKPIC2 Man page
groupFeaturesKPIC2,features-method Man page
groupFeaturesKPIC2,featuresSet-method Man page
groupFeaturesOpenMS Man page
groupFeaturesOpenMS,features-method Man page
groupFeaturesSIRIUS Man page Source code
groupFeaturesScreening Man page Source code
groupFeaturesXCMS Man page
groupFeaturesXCMS,features-method Man page
groupFeaturesXCMS,featuresSet-method Man page
groupFeaturesXCMS3 Man page
groupFeaturesXCMS3,features-method Man page
groupFeaturesXCMS3,featuresSet-method Man page
groupInfo Man page
groupInfo,featureGroups-method Man page
groupNames Man page
groupNames,MSPeakLists-method Man page
groupNames,components-method Man page
groupNames,compoundsCluster-method Man page
groupNames,featureAnnotations-method Man page
groupNames,featureGroups-method Man page
groupPseudoFeatures Source code
groupQualities Man page
groupQualities,featureGroups-method Man page
groupQualityFilter Source code
groupScores Man page
groupScores,featureGroups-method Man page
groupTable Man page
groupTable,featureGroups-method Man page
groups Man page Source code
hasFGroupScores Source code
hasName Source code
identifiers Man page
identifiers,compounds-method Man page
importCheckFeaturesSession Man page
importCheckUISessionGroups Source code
importConsensusXML Source code
importEnviPickPeakList Source code
importFeatureGroups Man page
importFeatureGroupsBrukerPA Man page Source code
importFeatureGroupsBrukerTASQ Man page Source code
importFeatureGroupsEnviMass Man page Source code
importFeatureGroupsKPIC2 Man page
importFeatureGroupsKPIC2FromFeat Source code
importFeatureGroupsXCMS Man page Source code
importFeatureGroupsXCMS3 Man page Source code
importFeatureGroupsXCMS3FromFeat Source code
importFeatureGroupsXCMSFromFeat Source code
importFeatureXML Source code
importFeatures Man page Source code
importFeaturesBrukerTASQ Source code
importFeaturesEnviMass Man page Source code
importFeaturesKPIC2 Man page Source code
importFeaturesXCMS Man page Source code
importFeaturesXCMS3 Man page Source code
importXCMSPeaks Source code
initCommand Source code
initMetFragCLCommand Source code
intensityFilter Source code
internalStandardAssignments Man page
internalStandardAssignments,featureGroups-method Man page
internalStandardAssignments,featureGroupsSet-method Man page
internalStandards Man page
internalStandards,featureGroups-method Man page
isEmptyMol Source code
isFGSet Source code
isLocalMetFragDB Source code
isSIRIUS5 Source code
isScreening Source code
isSuspAnnotated Source code
isValidMol Source code
isXCMSClass Source code
j Source code
jgc Source code
length Man page
length,MSLibrary-method Man page
length,MSPeakLists-method Man page
length,components-method Man page
length,compoundsCluster-method Man page
length,featureAnnotations-method Man page
length,featureGroups-method Man page
length,featureGroupsComparison-method Man page
length,features-method Man page
length,optimizationResult-method Man page
length,transformationProducts-method Man page
lengths Man page
lengths,compoundsCluster-method Man page
lengths,optimizationResult-method Man page
listMSFiles Source code
loadCacheData Man page Source code
loadCacheSet Source code
loadEICIntensities Source code
loadEICs Source code
loadIntensities Source code
loadMSLibrary Man page Source code
loadMSLibraryMSP Man page Source code
loadMSLibraryMoNAJSON Man page Source code
loadNewProjectParams Source code
loadRData Source code
loadSIRFeat Source code
loadSIRIUSFingerprints Source code
loadSpectra Source code
loadTASQFile Source code
loadXCMSRaw Source code
makeAlgoAdducts Source code
makeAnnDetailsReact Source code
makeAnnKable Source code
makeAnnPLReact Source code
makeAnnTitleTab Source code
makeCachedPlot Source code
makeClassHierarchy Source code
makeCommandList Source code
makeDAEIC Source code
makeDBIDsUnique Source code
makeDBIdentLink Source code
makeEmptyListNamed Source code
makeFGReactable Source code
makeFGroupName Source code
makeFeatAnnSetConsensus Source code
makeFileHash Man page Source code
makeGenFormCmdQueue Source code
makeGenFormFilesNames Source code
makeGraph Source code
makeHCluster Man page
makeHCluster,compounds-method Man page
makeHTMLReportPlot Source code
makeHTMLReportPlotOld Source code
makeHash Man page Source code
makeKPIC2PeakInfo Source code
makePropReactable Source code
makePropTab Source code
makeReactable Source code
makeReactableCompact Source code
makeSAFDInput Source code
makeSet Man page
makeSet,featureGroups-method Man page
makeSet,featureGroupsSet-method Man page
makeSet,features-method Man page
makeSet,featuresSet-method Man page
makeSetAlgorithm Source code
makeSirMSFile Source code
makeVennPlot Source code
makeXCMSGroups Source code
maxToxFilter Source code
maybeRestartCommand Source code
mdprintf Source code
memoise Source code
merge,MSLibrary,MSLibrary-method Man page
mergeAnaSubsetArgWithSets Source code
mergeComponents Source code
mergeFragInfo Source code
mergeScreeningSetInfos Source code
minAnalysesFilter Source code
minConcFilter Source code
minFeaturesFilter Source code
minReplicatesFilter Source code
minSetsFGroupsFilter Source code
mkdirp Source code
moveLastDTColumn Source code
names Man page
names,MSLibrary-method Man page
names,components-method Man page
names,featureGroups-method Man page
names,featureGroupsComparison-method Man page
names,transformationProducts-method Man page
neutralizeFeatures Source code
newProject Man page Source code
normInts Man page
normInts,featureGroups-method Man page
normInts,featureGroupsSet-method Man page
normalize Source code
normalizeAdducts Source code
normalizeAnnScores Source code
numEQ Source code
numGTE Source code
numLTE Source code
numericIDLevel Man page Source code
openCacheDB Source code
openProgBar Source code
optimizationResult Man page
optimizationResult-class Man page
optimizeFeatureFinding Man page Source code
optimizeFeatureGrouping Man page Source code
optimizePngPlots Source code
optimizedObject Man page
optimizedObject,optimizationResult-method Man page
optimizedParameters Man page
optimizedParameters,optimizationResult-method Man page
orderComponentsNames Source code
overlap Man page
overlap,featureGroups-method Man page
overlap,featureGroupsSet-method Man page
parents Man page
parents,transformationProducts-method Man page
parseAdductConsXMLFile Source code
parseFeatConsXMLFile Source code
parseFeatureXMLFile Source code
patRoon Man page
patRoon-defunct Man page
patRoon-deprecated Man page
patRoon-package Man page
peakLists Man page
peakLists,MSPeakLists-method Man page
plot Man page
plot,componentsClust,missing-method Man page
plot,compoundsCluster,missing-method Man page
plot,featureGroups,missing-method Man page
plot,featureGroupsComparison,missing-method Man page
plot,optimizationResult,missing-method Man page
plotBPCs Man page Man page Man page Man page
plotBPCs,data.frame-method Man page
plotBPCs,featureGroups-method Man page
plotBPCs,features-method Man page
plotChord Man page
plotChord,featureGroups-method Man page
plotChord,featureGroupsComparison-method Man page
plotChroms Man page
plotChroms,components-method Man page
plotChroms,featureGroups-method Man page
plotEIC Man page Source code
plotGraph Man page
plotGraph,componentsNT-method Man page
plotGraph,componentsNTSet-method Man page
plotGraph,componentsTPs-method Man page
plotGraph,featureGroups-method Man page
plotGraph,featureGroupsSet-method Man page
plotGraph,transformationProductsFormula-method Man page
plotGraph,transformationProductsStructure-method Man page
plotHeatMap Man page
plotHeatMap,componentsIntClust-method Man page
plotInt Man page
plotInt,componentsIntClust-method Man page
plotInt,featureGroups-method Man page
plotInt,featureGroupsSet-method Man page
plotScores Man page
plotScores,compounds-method Man page
plotScores,formulas-method Man page
plotSilhouettes Man page
plotSilhouettes,componentsClust-method Man page
plotSilhouettes,compoundsCluster-method Man page
plotSpec Man page Source code
plotSpectrum Man page
plotSpectrum,MSPeakLists-method Man page
plotSpectrum,MSPeakListsSet-method Man page
plotSpectrum,components-method Man page
plotSpectrum,compounds-method Man page
plotSpectrum,compoundsSet-method Man page
plotSpectrum,formulas-method Man page
plotSpectrum,formulasSet-method Man page
plotStructure Man page
plotStructure,compounds-method Man page
plotStructure,compoundsCluster-method Man page
plotTICs Man page Man page Man page Man page
plotTICs,data.frame-method Man page
plotTICs,featureGroups-method Man page
plotTICs,features-method Man page
plotUpSet Man page
plotUpSet,featureAnnotations-method Man page
plotUpSet,featureGroups-method Man page
plotUpSet,featureGroupsComparison-method Man page
plotUpSet,transformationProductsStructure-method Man page
plotVenn Man page
plotVenn,featureAnnotations-method Man page
plotVenn,featureGroups-method Man page
plotVenn,featureGroupsComparison-method Man page
plotVenn,featureGroupsSet-method Man page
plotVenn,transformationProductsStructure-method Man page
plotVolcano Man page
plotVolcano,featureGroups-method Man page
pred-aggr-params Man page
pred-quant Man page
pred-tox Man page
predictCheckFeaturesSession Man page
predictRespFactors Man page
predictRespFactors,compounds-method Man page
predictRespFactors,compoundsSIRIUS-method Man page
predictRespFactors,compoundsSet-method Man page
predictRespFactors,featureGroupsScreening-method Man page
predictRespFactors,featureGroupsScreeningSet-method Man page
predictRespFactors,formulasSIRIUS-method Man page
predictRespFactors,formulasSet-method Man page
predictTox Man page
predictTox,compounds-method Man page
predictTox,compoundsSIRIUS-method Man page
predictTox,compoundsSet-method Man page
predictTox,featureGroupsScreening-method Man page
predictTox,featureGroupsScreeningSet-method Man page
predictTox,formulasSIRIUS-method Man page
predictTox,formulasSet-method Man page
prepareChemTable Source code
prepareDTForComparison Source code
prepareMakeSetAdducts Source code
prepareReportPath Source code
prepareSuspectList Source code
printClassHierarchy Source code
printComponentsFiltered Source code
printFeatStats Source code
printPackageOpts Man page Source code
printf Source code
processGenFormMSMSResultFile Source code
processGenFormResultFile Source code
processMFResults Source code
processSIRIUSCompounds Source code
processSIRIUSFGroups Source code
processSIRIUSFormulas Source code
products Man page
products,transformationProducts-method Man page
pruneList Source code
rankFormulaTable Source code
reGenerateFTIndex Source code
reactExactFilter Source code
reactSelFilterButton Source code
reactSelectFilter Source code
reactSuspectFilter Source code
readAllFile Source code
readCheckSession Source code
readMSDataForXCMS3 Source code
readMSP Source code
readMoNAJSON Source code
readYAML Source code
recalibrarateDAFiles Man page Source code
records Man page
records,MSLibrary-method Man page
recursiveApplyDT Source code
removeDTColumnsIfPresent Source code
replicateAbundanceFilter Source code
replicateGroupFilter Source code
replicateGroupSubtract Man page
replicateGroupSubtract,featureGroups-method Man page
replicateGroups Man page
replicateGroups,featureGroups-method Man page
replicateGroups,features-method Man page
report Man page
report,featureGroups-method Man page
reportCSV Man page
reportCSV,featureGroups-method Man page
reportComponentPlots Source code
reportComponentTable Source code
reportCompoundClusters Source code
reportCompoundSpectra Source code
reportCompoundTable Source code
reportFGroupPlots Source code
reportFGroupTable Source code
reportFeatureTable Source code
reportFormulaSpectra Source code
reportFormulaTable Source code
reportHTML Man page
reportHTML,featureGroups-method Man page
reportMD Man page Source code
reportPDF Man page
reportPDF,featureGroups-method Man page
reporting Man page
reporting-legacy Man page
resultsFilter Source code
retentionMzFilter Source code
revertDAAnalyses Man page Source code
roundFGTab Source code
runCTS Source code
runCheckUI Source code
runGenForm Source code
runSIRIUS Source code
sanitizeMSLibrary Source code
saveCacheData Man page Source code
saveCacheSet Source code
saveCheckSession Source code
saveNewProjectParams Source code
saveRCDKStructure Source code
saveUISettings Source code
scoreFeatQuality Source code
scores Man page
scores,optimizationResult-method Man page
screenInfo Man page
screenInfo,featureGroupsScreening-method Man page
screenInfo,featureGroupsScreeningSet-method Man page
screenSuspects Man page
screenSuspects,featureGroups-method Man page
screenSuspects,featureGroupsScreening-method Man page
screenSuspects,featureGroupsScreeningSet-method Man page
screenSuspects,featureGroupsSet-method Man page
selectIons Man page
selectIons,featureGroups-method Man page
selectIons,featureGroupsSet-method Man page
setDAMethod Man page Source code
setFormulaPLID Source code
setMethodMult Source code
setObjects Man page
setObjects,workflowStepSet-method Man page
setReactNumRangeFilters Source code
setReactSelRangeFilter Source code
sets Man page
sets,featureGroupsSet-method Man page
sets,featuresSet-method Man page
sets,workflowStepSet-method Man page
sets-workflow Man page
settings Man page
settings,compoundsMF-method Man page
show Man page
show,MSLibrary-method Man page
show,MSPeakLists-method Man page
show,MSPeakListsSet-method Man page
show,adduct-method Man page
show,components-method Man page
show,componentsFeatures-method Man page
show,componentsSet-method Man page
show,compounds-method Man page
show,compoundsCluster-method Man page
show,compoundsSet-method Man page
show,featureGroups-method Man page
show,featureGroupsScreening-method Man page
show,featureGroupsScreeningSet-method Man page
show,featureGroupsSet-method Man page
show,features-method Man page
show,featuresSet-method Man page
show,formulas-method Man page
show,formulasSet-method Man page
show,optimizationResult-method Man page
show,transformationProducts-method Man page
show,workflowStep-method Man page
show,workflowStepSet-method Man page
showAnaInfo Source code
showDataAnalysis Man page Source code
showObjectSize Source code
simplifyAnalysisNames Source code
simplifyDAFormula Source code
simplifyFormula Source code
sortFormula Source code
specDistMatrix Source code
specDistRect Source code
specSimParams Man page
spectra Man page
spectra,MSLibrary-method Man page
spectrumSimilarity Man page
spectrumSimilarity,MSPeakLists-method Man page
spectrumSimilarity,MSPeakListsSet-method Man page
splitInBatches Source code
splitInNBatches Source code
subscriptFormula Source code
subscriptFormulaHTML Source code
subsetDTColumnsIfPresent Source code
subtractFormula Source code
suspAnnCols Source code
suspMetaDataCols Source code
suspect-screening Man page
syncComponentsSetObjects Source code
syncMSPeakListsSetObjects Source code
syncScreeningSetObjects Source code
tabularRD Source code
toxicities Man page
toxicities,featureGroups-method Man page
transformationProducts Man page
transformationProducts-class Man page
transformationProductsBT Man page
transformationProductsBT-class Man page
transformationProductsCTS Man page
transformationProductsCTS-class Man page
transformationProductsFormula Man page
transformationProductsFormula-class Man page
transformationProductsLibrary Man page
transformationProductsLibrary-class Man page
transformationProductsLibraryFormula Man page
transformationProductsLibraryFormula-class Man page
transformationProductsLogic Man page
transformationProductsLogic-class Man page
transformationProductsStructure Man page
transformationProductsStructure-class Man page
transformationProductsStructureConsensus Man page
transformationProductsStructureConsensus-class Man page
treeCut Man page
treeCut,componentsClust-method Man page
treeCut,compoundsCluster-method Man page
treeCutDynamic Man page
treeCutDynamic,componentsClust-method Man page
treeCutDynamic,compoundsCluster-method Man page
unFactorDF Source code
unifyLibNames Source code
unifyMFNames Source code
unifySirNames Source code
unique Man page
unique,featureGroups-method Man page
unique,featureGroupsSet-method Man page
unset Man page
unset,MSPeakListsSet-method Man page
unset,componentsNTSet-method Man page
unset,componentsSet-method Man page
unset,compoundsConsensusSet-method Man page
unset,compoundsSet-method Man page
unset,featureGroupsScreeningSet-method Man page
unset,featureGroupsSet-method Man page
unset,featuresSet-method Man page
unset,formulasConsensusSet-method Man page
unset,formulasSet-method Man page
updatePICSet Source code
verboseCall Source code
verifyCompNotAltered Source code
verifyDependencies Man page Source code
verifyFormulas Source code
verifyNoAdductIonizationArg Source code
withOpt Man page
withProg Source code
workflowStep Man page
workflowStep-class Man page
workflowStepSet Man page
workflowStepSet-class Man page
wrapStr Source code
writeFeatureXML Source code
writeGenFormFiles Source code
writeMSPLibrary Source code
writeYAML Source code
zeroToNULL Source code
rickhelmus/patRoon documentation built on April 3, 2024, 6:56 p.m.

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