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

Global functions
$,components-method Man page
$,compounds-method Man page
$,featureGroups-method Man page
$,featureGroupsComparison-method Man page
$,features-method Man page
$,formulaConsensus-method Man page
GUI-utils Man page
MSPeakLists Man page
MSPeakLists-class Man page
MSPeakLists-generation Man page
[,MSPeakLists,ANY,ANY,missing-method Man page
[,components,ANY,ANY,missing-method Man page
[,compounds,ANY,missing,missing-method Man page
[,compoundsCluster,ANY,missing,missing-method Man page
[,featureGroups,ANY,ANY,missing-method Man page
[,featureGroupsComparison,ANY,missing,missing-method Man page
[,features,ANY,missing,missing-method Man page
[,formulaConsensus,ANY,missing,missing-method Man page
[,formulas,ANY,ANY,missing-method Man page
[[,MSPeakLists,ANY,ANY-method Man page
[[,components,ANY,ANY-method Man page
[[,compounds,ANY,missing-method Man page
[[,featureGroups,ANY,ANY-method Man page
[[,featureGroupsComparison,ANY,missing-method Man page
[[,features,ANY,missing-method Man page
[[,formulaConsensus,ANY,missing-method Man page
[[,formulas,ANY,ANY-method Man page
aapply Source code
abundanceFilter Source code
addAllDAEICs Man page Source code
addDAEIC Man page Source code
addFormula Source code
addFormulaScoring Man page
addFormulaScoring,compounds-method Man page
algorithm Man page
algorithm,MSPeakLists-method Man page
algorithm,components-method Man page
algorithm,compounds-method Man page
algorithm,formulaConsensus-method Man page
algorithm,formulas-method Man page
algorithm,optimizationResult-method Man page
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,featureGroups-method Man page
analysisInfo,features-method Man page
assertAnalysisInfo Source code
assertAvgPListParams Source code
assertCanCreateDir Source code
assertCanCreateDirs Source code
assertMultiProcArgs Source code
assertNormalizationMethod Source code
assertOptimArgs Source code
averageMSPeakLists Source code
averageSpectra Source code
averageSpectraMZR Source code
averagedPeakLists,MSPeakLists-method Man page
baseName Source code
blankFilter Source code
bruker-utils Man page
buildMFLandingURL Source code
calculateIonFormula Source code
checkCSVFile Source code
checkChoiceSilent Source code
checkChromatograms Man page
checkChromatograms,featureGroups-method Man page
checkExtractArg Source code
checkHasNames Source code
checkPackage Source code
checkRange Source code
checkSubsetArg Source code
chromWidthFilter Source code
cleanFragFormulas Source code
clearCache Man page Source code
closeCacheDB Source code
closeDAFile Source code
clusterProperties Man page
clusterProperties,componentsIntClust-method Man page
clusterProperties,compoundsCluster-method Man page
clusters Man page
clusters,componentsIntClust-method Man page
clusters,compoundsCluster-method Man page
comparison Man page
comparison,featureGroups-method Man page
component-generation 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
componentsIntClust Man page
componentsIntClust-class Man page
compound-generation Man page
compoundTable Man page
compoundTable,compounds-method Man page
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
compoundsMF Man page
compoundsMF-class Man page
consensus Man page
consensus,components-method Man page
consensus,compounds-method Man page
consensus,featureGroupsComparison-method Man page
consensus,formulas-method Man page
consensusForFormulaList Source code
convertFeatureGroupsToFeatures Source code
convertMSFiles Man page Source code
convertMSFilesOpenMS Source code
convertMSFilesPWiz Source code
countCharInStr Source code
createCOMReference Man page Source code
curTimeMS Source code
cutClusters Man page
cutClusters,componentsIntClust-method Man page
cutClusters,compoundsCluster-method Man page
deIsotopeMSPeakList Source code
defMultiProcErrorHandler Source code
defaultPkgOpts Source code
doCreateProject Source code
doDynamicTreeCut Source code
doFilter Source code
doMSPeakListFilter Source code
emptyMol Source code
executeCommand Source code
executeMultiProcess Source code
experimentInfo,optimizationResult-method Man page
export Man page
export,featureGroups-method Man page
exportDAFiles Man page Source code
extractPAGroupInfo Source code
feature-filtering Man page
feature-finding Man page
feature-grouping Man page
feature-optimization Man page
featureGroups Man page
featureGroups-class Man page
featureGroups-compare Man page
featureGroupsBruker Man page
featureGroupsBruker-class Man page
featureGroupsComparison Man page
featureGroupsComparison-class Man page
featureGroupsEnviMass Man page
featureGroupsEnviMass-class Man page
featureGroupsOpenMS Man page
featureGroupsOpenMS-class Man page
featureGroupsXCMS Man page
featureGroupsXCMS-class Man page
featureTable Man page
featureTable,featureGroups-method Man page
featureTable,features-method Man page
features Man page
features-class Man page
featuresBruker Man page
featuresBruker-class Man page
featuresEnviPick Man page
featuresEnviPick-class Man page
featuresOpenMS Man page
featuresOpenMS-class Man page
featuresXCMS Man page
featuresXCMS-class Man page
filter Man page
filter,MSPeakLists-method Man page
filter,compounds-method Man page
filter,featureGroups-method Man page
filter,features-method Man page
findFGroup Man page
findFGroup,components-method Man page
findFeatures Man page Source code
findFeaturesBruker Man page Source code
findFeaturesEnviPick Man page Source code
findFeaturesOpenMS Man page Source code
findFeaturesXCMS Man page Source code
fixOptParamRange Source code
formConsensusColOrder Source code
formulaConsensus Man page
formulaConsensus-class Man page
formulaListToString Source code
formulaScoringColumns Source code
formulaTable Man page
formulaTable,formulaConsensus-method Man page
formulaTable,formulas-method Man page
formulas Man page
formulas-class Man page
genIntComponentInfo Source code
genIntComponents Source code
generateAnalysisInfo Man page Source code
generateAnalysisInfoFromEnviMass Man page Source code
generateComponents Man page
generateComponents,featureGroups-method Man page
generateComponentsCAMERA Man page Source code
generateComponentsIntClust Man page Source code
generateComponentsNontarget Man page Source code
generateComponentsRAMClustR Man page Source code
generateCompounds Man page
generateCompounds,featureGroups-method Man page
generateCompoundsMetfrag Man page Source code
generateCompoundsSirius Man page Source code
generateDACompounds Source code
generateFGroupsOptPSet Man page Source code
generateFGroupsOptPSetOpenMS Source code
generateFGroupsOptPSetXCMS Source code
generateFeatureOptPSet Man page Source code
generateFeatureOptPSetEnviPick Source code
generateFeatureOptPSetOpenMS Source code
generateFeatureOptPSetXCMS Source code
generateFormulasDA Source code
generateFormulasGenForm Source code
generateFormulasSirius Source code
generateMSPeakLists Man page
generateMSPeakLists,featureGroups-method Man page
generateMSPeakListsDA Man page Source code
generateMSPeakListsDAFMF Man page Source code
generateMSPeakListsMzR Man page Source code
generateMetFragRunData Source code
generics Man page
getAllCompCols Source code
getAnalysisPath Source code
getArgNames Source code
getBrewerPal Source code
getBrukerAnalysisPath Source code
getCSVStr Source code
getCacheFile Source code
getCacheMode Source code
getCommandWithOptPath Source code
getCompInfoList Source code
getCompInfoText Source code
getCompScoreColNames Source code
getCompSuspectListColNames Source code
getCompViewerUI 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
getDefFGroupsOptParamRanges Man page Source code
getDefFGroupsOptParamRangesOpenMS Source code
getDefFGroupsOptParamRangesXCMS Source code
getDefFeaturesOptParamRanges Man page Source code
getDefFeaturesOptParamRangesEnviPick Source code
getDefFeaturesOptParamRangesOpenMS Source code
getDefFeaturesOptParamRangesXCMS Source code
getEIC Source code
getEICUI Source code
getEICsForFGroups Source code
getElements Source code
getFeatIndicesFromPA Source code
getFeatIndicesFromXS Source code
getFeatures Man page
getFeatures,featureGroups-method Man page
getFormInfoList Source code
getFormulaFromSiriusFragFile Source code
getFragmentInfoFromForms Source code
getGenFormBin Source code
getMCS Man page
getMCS,compounds-method Man page
getMCS,compoundsCluster-method Man page
getMFFragmentInfo Source code
getMZFromMSPeakList Source code
getMaxCacheEntries Source code
getMoleculesFromSMILES Source code
getMostIntenseAnaWithMSMS Source code
getMzDataAnalysisPath Source code
getMzMLAnalysisPath Source code
getMzMLOrMzXMLAnalysisPath Source code
getMzXMLAnalysisPath Source code
getNewProjectUI Source code
getOpenMSFFCommand Source code
getScriptCode Source code
getSiriusBin Source code
getSiriusCommand Source code
getSiriusFragFiles Source code
getSpectraHeader Source code
getStrListWithMax Source code
getXCMSEiCHashFromPath Source code
getXCMSSet Man page
getXCMSSet,featureGroups-method Man page
getXCMSSet,featureGroupsXCMS-method Man page
getXCMSSet,features-method Man page
getXCMSSet,featuresOpenMS-method Man page
getXCMSSet,featuresXCMS-method Man page
groupFeatIndex Man page
groupFeatIndex,featureGroups-method Man page
groupFeatures Man page
groupFeatures,features-method Man page
groupFeaturesOpenMS Man page Source code
groupFeaturesScreening Man page
groupFeaturesScreening,featureGroups-method Man page
groupFeaturesXCMS Man page Source code
groupInfo Man page
groupInfo,featureGroups-method Man page
groupNames Man page
groupNames,MSPeakLists-method Man page
groupNames,components-method Man page
groupNames,compounds-method Man page
groupNames,compoundsCluster-method Man page
groupNames,featureGroups-method Man page
groupNames,formulaConsensus-method Man page
groupNames,formulas-method Man page
groupTable Man page
groupTable,featureGroups-method Man page
groups Man page
groups,featureGroups-method Man page
hasName Source code
identifiers Man page
identifiers,compounds-method Man page
importConsensusXML Source code
importConsensusXMLCpp Source code
importEnviPickPeakList Source code
importFeatureGroups Man page Source code
importFeatureGroupsBrukerPA Man page Source code
importFeatureGroupsBrukerTASQ Man page Source code
importFeatureGroupsEnviMass Man page Source code
importFeatureGroupsXCMS Man page Source code
importFeatureGroupsXCMSFromFeat Source code
importFeatureXML Source code
importFeatureXMLCpp Source code
importFeaturesBrukerTASQ Source code
importFeaturesEnviMass Man page Source code
importFeaturesXCMS Man page Source code
initGenFormFiles Source code
initMetFragCLCommand Source code
insertDFColumn Source code
insertDTColumn Source code
intensityFilter Source code
interReplicateAbundanceFilter Source code
intraReplicateFilter Source code
isEmptyMol Source code
isValidMol Source code
jgc Source code
length,MSPeakLists-method Man page
length,components-method Man page
length,compounds-method Man page
length,compoundsCluster-method Man page
length,featureGroups-method Man page
length,featureGroupsComparison-method Man page
length,features-method Man page
length,formulaConsensus-method Man page
length,formulas-method Man page
length,optimizationResult-method Man page
lengths,compoundsCluster-method Man page
lengths,optimizationResult-method Man page
line2user Source code
loadAllSpectra Source code
loadCacheData Source code
loadCacheSet Source code
loadEICIntensities Source code
loadEICs Source code
loadIntensities Source code
loadIntensitiesCPP Source code
loadRData Source code
loadSpectra Source code
loadXCMSEICForFGroups Source code
loadXCMSEICFromCache Source code
loadXCMSEICFromRaw Source code
loadXCMSRaw Source code
makeDAEIC Source code
makeFGroupName Source code
makeFileHash Source code
makeHCluster Man page
makeHCluster,compounds-method Man page
makeHash Source code
makeMSPlot Source code
makeMSPlotGG Source code
makeSirMSFile Source code
mergeFragInfo Source code
mkdirp Source code
names,components-method Man page
names,featureGroups-method Man page
names,featureGroupsComparison-method Man page
newProject Man page Source code
normalize Source code
normalizeCompScores Source code
numEQ Source code
numGTE Source code
numLTE Source code
onAttach Source code
onLoad Source code
openCacheDB Source code
optimizationResult Man page
optimizationResult-class Man page
optimizeFeatureFinding Man page Source code
optimizeFeatureGrouping Man page Source code
optimizePngPlots Source code
optimizedObject,optimizationResult-method Man page
optimizedParameters,optimizationResult-method Man page
overlap Man page
overlap,featureGroups-method Man page
parseFeatConsXMLFile Source code
parseFeatureXMLFile Source code
pasteNonEmpty Source code
patRoon Man page
patRoon-package Man page
peakLists Man page
peakLists,MSPeakLists-method Man page
plot,componentsIntClust,ANY-method Man page
plot,compoundsCluster,ANY-method Man page
plot,featureGroups,ANY-method Man page
plot,featureGroupsComparison,ANY-method Man page
plot,optimizationResult,ANY-method Man page
plotChord Man page
plotChord,featureGroups-method Man page
plotChord,featureGroupsComparison-method Man page
plotDendroWithClusters Source code
plotEIC Man page
plotEIC,components-method Man page
plotEIC,featureGroups-method Man page
plotFeatGroupEIC Source code
plotHeatMap Man page
plotHeatMap,componentsIntClust-method Man page
plotInt Man page
plotInt,componentsIntClust-method Man page
plotInt,featureGroups-method Man page
plotScores Man page
plotScores,compounds-method Man page
plotSilhouettes Man page
plotSilhouettes,componentsIntClust-method Man page
plotSpec Man page
plotSpec,MSPeakLists-method Man page
plotSpec,components-method Man page
plotSpec,compounds-method Man page
plotSpec,formulaConsensus-method Man page
plotStructure Man page
plotStructure,compounds-method Man page
plotStructure,compoundsCluster-method Man page
plotUpSet Man page
plotUpSet,featureGroups-method Man page
plotUpSet,featureGroupsComparison-method Man page
plotVenn Man page
plotVenn,featureGroups-method Man page
plotVenn,featureGroupsComparison-method Man page
plotXCMSEIC Source code
prepareReportPath Source code
printf Source code
processGenFormMSMSResultFile Source code
processGenFormResultFile Source code
processMFResults Source code
processSiriusCompounds Source code
processSiriusFormulas Source code
pruneList Source code
rcdkplot Source code
readAllFile Source code
recalibrarateDAFiles Man page Source code
recursiveApplyDT Source code
regression Man page
regression,featureGroups-method Man page
replicateGroupFilter Source code
replicateGroupSubtract Man page
replicateGroupSubtract,featureGroups-method Man page
replicateGroups Man page
replicateGroups,featureGroups-method Man page
replicateGroups,features-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
reportMD Man page
reportMD,featureGroups-method Man page
reportPDF Man page
reportPDF,featureGroups-method Man page
reporting Man page
retentionMzFilter Source code
saveCacheData Source code
saveCacheSet Source code
scores,optimizationResult-method Man page
screenTargets Man page
screenTargets,featureGroups-method Man page
screenTargets,features-method Man page
setDAMethod Man page Source code
settings Man page
settings,compoundsMF-method Man page
show,MSPeakLists-method Man page
show,components-method Man page
show,compounds-method Man page
show,compoundsCluster-method Man page
show,featureGroups-method Man page
show,features-method Man page
show,formulaConsensus-method Man page
show,formulas-method Man page
show,optimizationResult-method Man page
showAnaInfo Source code
showDataAnalysis Man page Source code
showObjectSize Source code
simplifyAnalysisNames Source code
simplifyDAFormula Source code
sortFormula Source code
splitFormulaToList Source code
stripDTRef Source code
subtractFormula Source code
target-screening Man page
treeCut Man page
treeCut,componentsIntClust-method Man page
treeCut,compoundsCluster-method Man page
treeCutDynamic Man page
treeCutDynamic,componentsIntClust-method Man page
treeCutDynamic,compoundsCluster-method Man page
unFactorDF Source code
unifyMFNames Source code
unifySirNames Source code
unique,featureGroups-method Man page
unique,featureGroupsComparison-method Man page
wrapStr Source code
writeFeatureXML Source code
rickhelmus/patRoon documentation built on Dec. 6, 2018, 3:39 a.m.