Man pages for bioFAM/MOFA
Multi-Omics Factor Analysis (MOFA)

calculateVarianceExplained	Calculate variance explained by the model
clusterSamples	clusterSamples: K-means clustering on samples based on latent...
compareFactors	Correlation of the latent factors across different trials
compareModels	Compare different instances of trained 'MOFAmodel'
createMOFAobject	Initialize a MOFA object
DataOptions	DataOptions: set and retrieve data options
Dimensions	Dimensions: set and retrieve dimensions
Expectations	Expectations: set and retrieve expectations of model...
factorNames	factorNames: set and retrieve factor names
FeatureIntercepts	FeatureIntercepts: set and retrieve feature intercepts
featureNames	featureNames: set and retrieve feature names
getCovariates	getCovariates
getDefaultDataOptions	Get default data options
getDefaultModelOptions	Get default model options
getDefaultTrainOptions	Get default training options
getDimensions	getDimensions
getELBO	getELBO
getExpectations	getExpectations
getFactors	getFactors
getImputedData	getImputedData
getTrainData	getTrainData
getWeights	getWeights
impute	Impute missing values from a fitted MOFA model
ImputedData	ImputedData: set and retrieve imputed data
InputData	InputData: set and retrieve input data
loadModel	loading a trained MOFA model
makeExampleData	make an example multi-view data set for illustration of MOFA
ModelOptions	ModelOptions: set and retrieve model options
MOFA	Multi-Omics Factor Analysis (MOFA)
MOFAmodel	Class to store a Multi-Omics Factor Analysis (MOFA) model
plotDataHeatmap	Plot heatmap of relevant features
plotDataOverview	Plot overview of the input data
plotDataScatter	Scatterplots of feature values against latent factors
plotEnrichment	Plot output of Feature Set Enrichment Analysis
plotEnrichmentBars	Barplot of Feature Set Enrichment Analysis results
plotEnrichmentDetailed	Plot detailed output of the Feature Set Enrichment Analysis
plotEnrichmentHeatmap	Heatmap of Feature Set Enrichment Analysis results
plotFactorBeeswarm	Beeswarm plot of latent factors
plotFactorCor	Plot correlation matrix between latent factors
plotFactorHist	Plot histogram of latent factor values
plotFactorScatter	Scatterplot of two latent factors
plotFactorScatters	Pairwise scatterplots of multiple latent factors
plotTopWeights	Plot top weights
plotVarianceExplained	Plot variance explained by the model
plotWeights	Plot Weights
plotWeightsHeatmap	Plot heatmap of the weights
predict	Do predictions using a fitted MOFA model
prepareMOFA	prepare a MOFAobject for training
qualityControl	qualityControl
regressCovariates	regress out a covariate from the training data
runEnrichmentAnalysis	Feature Set Enrichment Analysis
runMOFA	train a MOFA model
sampleNames	sampleNames: set and retrieve sample names
selectModel	Select the best model from a list of trained 'MOFAmodel'...
Status	Status: set and retrieve training status
subsetFactors	Subset factors
subsetSamples	Subset samples
subsetViews	Subset views
trainCurveELBO	Training curve for Evidence Lower Bound (ELBO)
trainCurveFactors	Training curve for the number of active factors
TrainData	TrainData: set and retrieve training data
TrainOptions	TrainOptions: set and retrieve training options
TrainStats	TrainStats: set and retrieve training statistcs
viewNames	viewNames: set and retrieve view names