MSstatsConvert-package	MSstatsConvert
.addFractions	dot-addFractions
.adjustIntensities	dot-adjustIntensities
.aggregatePSMstoPeptideIons	dot-aggregatePSMstoPeptideIons
.checkAnnotation	dot-checkAnnotation
.checkDDA	dot-checkDDA
.checkDuplicatedMeasurements	dot-checkDuplicatedMeasurements
.checkMSstatsParams	dot-checkMSstatsParams
.checkMultiRun	dot-checkMultiRun
.checkOverlappedFeatures	dot-checkOverlappedFeatures
.cleanByFeature	dot-cleanByFeature
.cleanRawDIANN	dot-cleanRawDIANN
.cleanRawDIAUmpire	dot-cleanRawDIAUmpire
.cleanRawMaxQuant	dot-cleanRawMaxQuant
.cleanRawMetamorpheus	dot-cleanRawMetamorpheus
.cleanRawOpenMS	dot-cleanRawOpenMS
.cleanRawOpenSWATH	dot-cleanRawOpenSWATH
.cleanRawPD	dot-cleanRawPD
.cleanRawPDMSstats	dot-cleanRawPDMSstats
.cleanRawPDTMT	dot-cleanRawPDTMT
.cleanRawPhilosopher	dot-cleanRawPhilosopher
.cleanRawProgenesis	dot-cleanRawProgenesis
.cleanRawSkyline	dot-cleanRawSkyline
.cleanRawSpectroMineTMT	dot-cleanRawSpectroMineTMT
.cleanRawSpectronaut	dot-cleanRawSpectronaut
.countCommonFeatures	dot-countCommonFeatures
.fillValues	dot-fillValues
.filterByPattern	dot-filterByPattern
.filterByScore	dot-filterByScore
.filterExact	dot-filterExact
.filterFewMeasurements	dot-filterFewMeasurements
.filterManyColumns	dot-filterManyColumns
.filterOverlapped	dot-filterOverlapped
.findAvailable	dot-findAvailable
.fixBasicColumns	dot-fixBasicColumns
.fixColumnTypes	dot-fixColumnTypes
.fixMissingValues	dot-fixMissingValues
.getChannelColumns	dot-getChannelColumns
.getCorrectFraction	dot-getCorrectFraction
.getDataTable	dot-getDataTable
.getFullDesign	dot-getFullDesign
.getMissingRunsPerFeature	dot-getMissingRunsPerFeature
.getOverlappingFeatures	dot-getOverlappingFeatures
.handleFiltering	dot-handleFiltering
.handleFractions	dot-handleFractions
.handleFractionsLF	dot-handleFractionsLF
.handleFractionsTMT	dot-handleFractionsTMT
.handleIsotopicPeaks	dot-handleIsotopicPeaks
.handleSharedPeptides	dot-handleSharedPeptides
.handleSingleFeaturePerProtein	dot-handleSingleFeaturePerProtein
.logConverterOptions	dot-logConverterOptions
.logSuccess	dot-logSuccess
.makeBalancedDesign	dot-makeBalancedDesign
.makeExactFilterMessage	dot-makeExactFilterMessage
.makeScoreFilterMessage	dot-makeScoreFilterMessage
.mergeAnnotation	dot-mergeAnnotation
.MSstatsFormat	dot-MSstatsFormat
.nullAppender	dot-nullAppender
.onLoad	dot-onLoad
.removeOverlappingFeatures	dot-removeOverlappingFeatures
.removeSharedPeptides	dot-removeSharedPeptides
.selectMSstatsColumns	dot-selectMSstatsColumns
.sharedParametersAmongConverters	dot-sharedParametersAmongConverters
.standardizeColnames	dot-standardizeColnames
.summarizeMultipleMeasurements	dot-summarizeMultipleMeasurements
.summarizeMultiplePSMs	dot-summarizeMultiplePSMs
.validatePDTMTInputColumns	dot-validatePDTMTInputColumns
as.data.frame.MSstatsValidated	as.data.frame.MSstatsValidated
as.data.table.MSstatsValidated	as.data.table.MSstatsValidated
DIANNtoMSstatsFormat	DIANNtoMSstatsFormat
DIAUmpiretoMSstatsFormat	DIAUmpiretoMSstatsFormat
FragPipetoMSstatsFormat	FragPipetoMSstatsFormat
getDataType	getDataType
getDataType,MSstatsInputFiles-method	getDataType
getInputFile	getInputFile
getInputFile,MSstatsInputFiles-method	getInputFile
getInputFile,MSstatsPhilosopherFiles-method	getInputFile
MaxQtoMSstatsFormat	MaxQtoMSstatsFormat
MetamorpheusToMSstatsFormat	MetamorpheusToMSstatsFormat
MSstatsBalancedDesign	MSstatsBalancedDesign
MSstatsClean	MSstatsClean
MSstatsClean,MSstatsDIANNFiles-method	MSstatsClean
MSstatsClean,MSstatsDIAUmpireFiles-method	MSstatsClean
MSstatsClean,MSstatsMaxQuantFiles-method	MSstatsClean
MSstatsClean,MSstatsMetamorpheusFiles-method	MSstatsClean
MSstatsClean,MSstatsOpenMSFiles-method	MSstatsClean
MSstatsClean,MSstatsOpenSWATHFiles-method	MSstatsClean
MSstatsClean,MSstatsPhilosopherFiles-method	MSstatsClean
MSstatsClean,MSstatsProgenesisFiles-method	MSstatsClean
MSstatsClean,MSstatsProteinProspectorFiles-method	MSstatsClean
MSstatsClean,MSstatsProteomeDiscovererFiles-method	MSstatsClean
MSstatsClean,MSstatsSkylineFiles-method	MSstatsClean
MSstatsClean,MSstatsSpectroMineFiles-method	MSstatsClean
MSstatsClean,MSstatsSpectronautFiles-method	MSstatsClean
MSstatsConvert	MSstatsConvert
MSstatsDIANNFiles-class	MSstatsInputFiles
MSstatsDIAUmpireFiles-class	MSstatsInputFiles
MSstatsFragPipeFiles-class	MSstatsInputFiles
MSstatsImport	MSstatsImport
MSstatsInputFiles-class	MSstatsInputFiles
MSstatsLogsSettings	MSstatsLogsSettings
MSstatsMakeAnnotation	MSstatsMakeAnnotation
MSstatsMaxQuantFiles-class	MSstatsInputFiles
MSstatsMetamorpheusFiles-class	MSstatsInputFiles
MSstatsOpenMSFiles-class	MSstatsInputFiles
MSstatsOpenSWATHFiles-class	MSstatsInputFiles
MSstatsPhilosopherFiles-class	MSstatsInputFiles
MSstatsPreprocess	MSstatsPreprocess
MSstatsProgenesisFiles-class	MSstatsInputFiles
MSstatsProteinProspectorFiles-class	MSstatsInputFiles
MSstatsProteomeDiscovererFiles-class	MSstatsInputFiles
MSstatsSaveSessionInfo	MSstatsSaveSessionInfo
MSstatsSkylineFiles-class	MSstatsInputFiles
MSstatsSpectroMineFiles-class	MSstatsInputFiles
MSstatsSpectronautFiles-class	MSstatsInputFiles
OpenMStoMSstatsFormat	OpenMStoMSstatsFormat
OpenSWATHtoMSstatsFormat	OpenSWATHtoMSstatsFormat
PDtoMSstatsFormat	PDtoMSstatsFormat
ProgenesistoMSstatsFormat	ProgenesistoMSstatsFormat
ProteinProspectortoMSstatsTMTFormat	ProteinProspectortoMSstatsTMTFormat
SkylinetoMSstatsFormat	SkylinetoMSstatsFormat
SpectronauttoMSstatsFormat	SpectronauttoMSstatsFormat
