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

calculateVarianceExplainedCalculate variance explained by the model
clusterSamplesclusterSamples: K-means clustering on samples based on latent...
compareFactorsCorrelation of the latent factors across different trials
compareModelsCompare different instances of trained 'MOFAmodel'
createMOFAobjectInitialize a MOFA object
DataOptionsDataOptions: set and retrieve data options
DimensionsDimensions: set and retrieve dimensions
ExpectationsExpectations: set and retrieve expectations of model...
factorNamesfactorNames: set and retrieve factor names
FeatureInterceptsFeatureIntercepts: set and retrieve feature intercepts
featureNamesfeatureNames: set and retrieve feature names
getCovariatesgetCovariates
getDefaultDataOptionsGet default data options
getDefaultModelOptionsGet default model options
getDefaultTrainOptionsGet default training options
getDimensionsgetDimensions
getELBOgetELBO
getExpectationsgetExpectations
getFactorsgetFactors
getImputedDatagetImputedData
getTrainDatagetTrainData
getWeightsgetWeights
imputeImpute missing values from a fitted MOFA model
ImputedDataImputedData: set and retrieve imputed data
InputDataInputData: set and retrieve input data
loadModelloading a trained MOFA model
makeExampleDatamake an example multi-view data set for illustration of MOFA
ModelOptionsModelOptions: set and retrieve model options
MOFAMulti-Omics Factor Analysis (MOFA)
MOFAmodelClass to store a Multi-Omics Factor Analysis (MOFA) model
plotDataHeatmapPlot heatmap of relevant features
plotDataOverviewPlot overview of the input data
plotDataScatterScatterplots of feature values against latent factors
plotEnrichmentPlot output of Feature Set Enrichment Analysis
plotEnrichmentBarsBarplot of Feature Set Enrichment Analysis results
plotEnrichmentDetailedPlot detailed output of the Feature Set Enrichment Analysis
plotEnrichmentHeatmapHeatmap of Feature Set Enrichment Analysis results
plotFactorBeeswarmBeeswarm plot of latent factors
plotFactorCorPlot correlation matrix between latent factors
plotFactorHistPlot histogram of latent factor values
plotFactorScatterScatterplot of two latent factors
plotFactorScattersPairwise scatterplots of multiple latent factors
plotTopWeightsPlot top weights
plotVarianceExplainedPlot variance explained by the model
plotWeightsPlot Weights
plotWeightsHeatmapPlot heatmap of the weights
predictDo predictions using a fitted MOFA model
prepareMOFAprepare a MOFAobject for training
qualityControlqualityControl
regressCovariatesregress out a covariate from the training data
runEnrichmentAnalysisFeature Set Enrichment Analysis
runMOFAtrain a MOFA model
sampleNamessampleNames: set and retrieve sample names
selectModelSelect the best model from a list of trained 'MOFAmodel'...
StatusStatus: set and retrieve training status
subsetFactorsSubset factors
subsetSamplesSubset samples
subsetViewsSubset views
trainCurveELBOTraining curve for Evidence Lower Bound (ELBO)
trainCurveFactorsTraining curve for the number of active factors
TrainDataTrainData: set and retrieve training data
TrainOptionsTrainOptions: set and retrieve training options
TrainStatsTrainStats: set and retrieve training statistcs
viewNamesviewNames: set and retrieve view names
bioFAM/MOFA documentation built on Nov. 7, 2019, 11:01 p.m.