MOFA-package	MOFA
calculateVarianceExplained	calculateVarianceExplained
clusterSamples	clusterSamples
compareFactors	compareFactors
compareModels	compareModels
createMOFAobject	createMOFAobject
DataOptions	DataOptions
DataOptions,MOFAmodel-method	DataOptions
DataOptions<-	DataOptions
DataOptions<-,MOFAmodel,list-method	DataOptions
Dimensions	Dimensions
Dimensions,MOFAmodel-method	Dimensions
Dimensions<-	Dimensions
Dimensions<-,MOFAmodel,list-method	Dimensions
Expectations	Expectations
Expectations,MOFAmodel-method	Expectations
Expectations<-	Expectations
Expectations<-,MOFAmodel,list-method	Expectations
factorNames	factorNames
factorNames,MOFAmodel-method	factorNames
factorNames<-	factorNames
factorNames<-,MOFAmodel,vector-method	factorNames
FeatureIntercepts	FeatureIntercepts
FeatureIntercepts,MOFAmodel-method	FeatureIntercepts
FeatureIntercepts<-	FeatureIntercepts
FeatureIntercepts<-,MOFAmodel,list-method	FeatureIntercepts
featureNames	featureNames
featureNames,MOFAmodel-method	featureNames
featureNames<-	featureNames
featureNames<-,MOFAmodel,list-method	featureNames
getCovariates	getCovariates
getDefaultDataOptions	getDefaultDataOptions
getDefaultModelOptions	getDefaultModelOptions
getDefaultTrainOptions	getDefaultTrainOptions
getDimensions	getDimensions
getELBO	getELBO
getExpectations	getExpectations
getFactors	getFactors
getImputedData	getImputedData
getTrainData	getTrainData
getWeights	getWeights
impute	impute
ImputedData	ImputedData
ImputedData,MOFAmodel-method	ImputedData
ImputedData<-	ImputedData
ImputedData<-,MOFAmodel,list-method	ImputedData
InputData	InputData
InputData,MOFAmodel-method	InputData
InputData<-	InputData
InputData<-,MOFAmodel,MultiAssayExperiment-method	InputData
loadModel	loadModel
makeExampleData	makeExampleData
ModelOptions	ModelOptions
ModelOptions,MOFAmodel-method	ModelOptions
ModelOptions<-	ModelOptions
ModelOptions<-,MOFAmodel,list-method	ModelOptions
MOFA	MOFA
MOFAmodel	MOFAmodel
MOFAmodel-class	MOFAmodel
plotDataHeatmap	plotDataHeatmap
plotDataOverview	plotDataOverview
plotDataScatter	plotDataScatter
plotEnrichment	plotEnrichment
plotEnrichmentBars	plotEnrichmentBars
plotEnrichmentDetailed	plotEnrichmentDetailed
plotEnrichmentHeatmap	plotEnrichmentHeatmap
plotFactorBeeswarm	plotFactorBeeswarm
plotFactorCor	plotFactorCor
plotFactorHist	plotFactorHist
plotFactorScatter	plotFactorScatter
plotFactorScatters	plotFactorScatters
plotTopWeights	plotTopWeights
plotVarianceExplained	plotVarianceExplained
plotWeights	plotWeights
plotWeightsHeatmap	plotWeightsHeatmap
predict	predict
prepareMOFA	prepareMOFA
qualityControl	qualityControl
regressCovariates	regressCovariates
runEnrichmentAnalysis	runEnrichmentAnalysis
runMOFA	runMOFA
sampleNames	sampleNames
sampleNames,MOFAmodel-method	sampleNames
sampleNames<-	sampleNames
sampleNames<-,MOFAmodel,vector-method	sampleNames
selectModel	selectModel
Status	Status
Status,MOFAmodel-method	Status
Status<-	Status
Status<-,MOFAmodel,character-method	Status
subsetFactors	subsetFactors
subsetSamples	subsetSamples
subsetViews	subsetViews
trainCurveELBO	trainCurveELBO
trainCurveFactors	trainCurveFactors
TrainData	TrainData
TrainData,MOFAmodel-method	TrainData
TrainData<-	TrainData
TrainData<-,MOFAmodel,list-method	TrainData
TrainOptions	TrainOptions
TrainOptions,MOFAmodel-method	TrainOptions
TrainOptions<-	TrainOptions
TrainOptions<-,MOFAmodel,list-method	TrainOptions
TrainStats	TrainStats
TrainStats,MOFAmodel-method	TrainStats
TrainStats<-	TrainStats
TrainStats<-,MOFAmodel,list-method	TrainStats
viewNames	viewNames
viewNames,MOFAmodel-method	viewNames
viewNames<-	viewNames
viewNames<-,MOFAmodel,character-method	viewNames
