.addCoverageInfo	dot-addCoverageInfo
.addModelInformation	dot-addModelInformation
.addModelVariances	dot-addModelVariances
.addNInformativeInfo	dot-addNInformativeInfo
.addNoisyFlag	dot-addNoisyFlag
.addOutlierCutoff	dot-addOutlierCutoff
.addOutlierInformation	dot-addOutlierInformation
.addSurvivalPredictions	dot-addSurvivalPredictions
.adjustLRuns	dot-adjustLRuns
.calculateOutlierCutoff	dot-calculateOutlierCutoff
.calculatePower	dot-calculatePower
.calculateProteinVariance	dot-calculateProteinVariance
.checkContrastMatrix	dot-checkContrastMatrix
.checkDataProcessParams	dot-checkDataProcessParams
.checkExperimentDesign	dot-checkExperimentDesign
.checkGCPlotsInput	dot-checkGCPlotsInput
.checkGroupComparisonInput	dot-checkGroupComparisonInput
.checkSingleFeature	dot-checkSingleFeature
.checkSingleLabelProteins	dot-checkSingleLabelProteins
.checkSingleSubject	dot-checkSingleSubject
.checkTechReplicate	dot-checkTechReplicate
.checkUnProcessedDataValidity	dot-checkUnProcessedDataValidity
.countInformative	dot-countInformative
.countMissingPercentage	dot-countMissingPercentage
.documentFunction	dot-documentFunction
.finalizeInput	dot-finalizeInput
.finalizeLinear	dot-finalizeLinear
.finalizeTMP	dot-finalizeTMP
.fitHuber	dot-fitHuber
.fitLinearModel	dot-fitLinearModel
.fitModelForGroupComparison	dot-fitModelForGroupComparison
.fitModelSingleProtein	dot-fitModelSingleProtein
.fitTukey	dot-fitTukey
.flagLowCoverage	dot-flagLowCoverage
.flagUninformativeSingleLabel	dot-flagUninformativeSingleLabel
.getAllComparisons	dot-getAllComparisons
.getContrast	dot-getContrast
.getContrastLabels	dot-getContrastLabels
.getEmptyComparison	dot-getEmptyComparison
.getFeatureVariances	dot-getFeatureVariances
.getMedian	dot-getMedian
.getMedianSigmaSubject	dot-getMedianSigmaSubject
.getMin	dot-getMin
.getModelParameters	dot-getModelParameters
.getNonMissingFilter	dot-getNonMissingFilter
.getNonMissingFilterStats	dot-getNonMissingFilterStats
.getNumSample	dot-getNumSample
.getSingleProteinForProfile	dot-getSingleProteinForProfile
.getVarComponent	dot-getVarComponent
.getWideTable	dot-getWideTable
.getYaxis	dot-getYaxis
.handleEmptyConditions	dot-handleEmptyConditions
.handleSingleContrast	dot-handleSingleContrast
.isSummarizable	dot-isSummarizable
.logDatasetInformation	dot-logDatasetInformation
.logMissingness	dot-logMissingness
.logSingleLabeledProteins	dot-logSingleLabeledProteins
.logSummaryStatistics	dot-logSummaryStatistics
.makeComparison	dot-makeComparison
.makeConditionPlot	dot-makeConditionPlot
.makeFactorColumns	dot-makeFactorColumns
.makeHeatmap	dot-makeHeatmap
.makeProfilePlot	dot-makeProfilePlot
.makeQCPlot	dot-makeQCPlot
.makeSummaryProfilePlot	dot-makeSummaryProfilePlot
.makeVolcano	dot-makeVolcano
.nicePrint	dot-nicePrint
.normalizeGlobalStandards	dot-normalizeGlobalStandards
.normalizeMedian	dot-normalizeMedian
.normalizeQuantile	dot-normalizeQuantile
.onLoad	dot-onLoad
.plotComparison	dot-plotComparison
.plotHeatmap	dot-plotHeatmap
.plotVolcano	dot-plotVolcano
.prepareForDataProcess	dot-prepareForDataProcess
.prepareLinear	dot-prepareLinear
.prepareSingleProteinForGC	dot-prepareSingleProteinForGC
.prepareSummary	dot-prepareSummary
.prepareTMP	dot-prepareTMP
.preProcessIntensities	dot-preProcessIntensities
.quantileNormalizationSingleLabel	dot-quantileNormalizationSingleLabel
.replaceZerosWithNA	dot-replaceZerosWithNA
.runTukey	dot-runTukey
.saveSessionInfo	dot-saveSessionInfo
.saveTable	dot-saveTable
.selectHighQualityFeatures	dot-selectHighQualityFeatures
.selectTopFeatures	dot-selectTopFeatures
.setCensoredByThreshold	dot-setCensoredByThreshold
.updateColumnsForProcessing	dot-updateColumnsForProcessing
.updateUnequalVariances	dot-updateUnequalVariances
checkRepeatedDesign	checkRepeatedDesign
dataProcess	dataProcess
dataProcessPlots	dataProcessPlots
DDARawData	DDARawData
DDARawData.Skyline	DDARawData.Skyline
designSampleSize	designSampleSize
designSampleSizePlots	designSampleSizePlots
DIARawData	DIARawData
DIAUmpiretoMSstatsFormat	DIAUmpiretoMSstatsFormat
getProcessed	getProcessed
getSamplesInfo	getSamplesInfo
getSelectedProteins	getSelectedProteins
groupComparison	groupComparison
groupComparisonPlots	groupComparisonPlots
makePeptidesDictionary	makePeptidesDictionary
MaxQtoMSstatsFormat	MaxQtoMSstatsFormat
modelBasedQCPlots	modelBasedQCPlots
MSstatsContrastMatrix	MSstatsContrastMatrix
MSstatsGroupComparison	MSstatsGroupComparison
MSstatsGroupComparisonOutput	MSstatsGroupComparisonOutput
MSstatsGroupComparisonSingleProtein	MSstatsGroupComparisonSingleProtein
MSstatsHandleMissing	MSstatsHandleMissing
MSstatsMergeFractions	MSstatsMergeFractions
MSstatsNormalize	MSstatsNormalize
MSstatsPrepareForDataProcess	MSstatsPrepareForDataProcess
MSstatsPrepareForGroupComparison	MSstatsPrepareForGroupComparison
MSstatsPrepareForSummarization	MSstatsPrepareForSummarization
MSstatsSelectFeatures	MSstatsSelectFeatures
MSstatsSummarizationOutput	MSstatsSummarizationOutput
MSstatsSummarize	MSstatsSummarize
MSstatsSummarizeSingleLinear	MSstatsSummarizeSingleLinear
MSstatsSummarizeSingleTMP	MSstatsSummarizeSingleTMP
OpenMStoMSstatsFormat	OpenMStoMSstatsFormat
OpenSWATHtoMSstatsFormat	OpenSWATHtoMSstatsFormat
PDtoMSstatsFormat	PDtoMSstatsFormat
ProgenesistoMSstatsFormat	ProgenesistoMSstatsFormat
quantification	quantification
savePlot	savePlot
SkylinetoMSstatsFormat	SkylinetoMSstatsFormat
SpectronauttoMSstatsFormat	SpectronauttoMSstatsFormat
SRMRawData	SRMRawData
theme_msstats	theme_msstats
