| MOFA-package | Multi-Omics Factor Analysis (MOFA) |
| calculateVarianceExplained | Calculate variance explained by the model |
| clusterSamples | clusterSamples: K-means clustering on samples based on latent factors |
| 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 |
| DataOptions-method | DataOptions: set and retrieve data options |
| DataOptions<- | DataOptions: set and retrieve data options |
| DataOptions<--method | DataOptions: set and retrieve data options |
| Dimensions | Dimensions: set and retrieve dimensions |
| Dimensions-method | Dimensions: set and retrieve dimensions |
| Dimensions<- | Dimensions: set and retrieve dimensions |
| Dimensions<--method | Dimensions: set and retrieve dimensions |
| Expectations | Expectations: set and retrieve expectations of model components |
| Expectations-method | Expectations: set and retrieve expectations of model components |
| Expectations<- | Expectations: set and retrieve expectations of model components |
| Expectations<--method | Expectations: set and retrieve expectations of model components |
| factorNames | factorNames: set and retrieve factor names |
| factorNames-method | factorNames: set and retrieve factor names |
| factorNames<- | factorNames: set and retrieve factor names |
| factorNames<--method | factorNames: set and retrieve factor names |
| FeatureIntercepts | FeatureIntercepts: set and retrieve feature intercepts |
| FeatureIntercepts-method | FeatureIntercepts: set and retrieve feature intercepts |
| FeatureIntercepts<- | FeatureIntercepts: set and retrieve feature intercepts |
| FeatureIntercepts<--method | FeatureIntercepts: set and retrieve feature intercepts |
| featureNames | featureNames: set and retrieve feature names |
| featureNames-method | featureNames: set and retrieve feature names |
| featureNames<- | featureNames: set and retrieve feature names |
| featureNames<--method | 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 |
| ImputedData-method | ImputedData: set and retrieve imputed data |
| ImputedData<- | ImputedData: set and retrieve imputed data |
| ImputedData<--method | ImputedData: set and retrieve imputed data |
| InputData | InputData: set and retrieve input data |
| InputData-method | InputData: set and retrieve input data |
| InputData<- | InputData: set and retrieve input data |
| InputData<--method | 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 |
| ModelOptions-method | ModelOptions: set and retrieve model options |
| ModelOptions<- | ModelOptions: set and retrieve model options |
| ModelOptions<--method | ModelOptions: set and retrieve model options |
| MOFA | Multi-Omics Factor Analysis (MOFA) |
| MOFAmodel | Class to store a Multi-Omics Factor Analysis (MOFA) model |
| MOFAmodel-class | 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 |
| sampleNames-method | sampleNames: set and retrieve sample names |
| sampleNames<- | sampleNames: set and retrieve sample names |
| sampleNames<--method | sampleNames: set and retrieve sample names |
| selectModel | Select the best model from a list of trained 'MOFAmodel' objects |
| Status | Status: set and retrieve training status |
| Status-method | Status: set and retrieve training status |
| Status<- | Status: set and retrieve training status |
| Status<--method | 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 |
| TrainData-method | TrainData: set and retrieve training data |
| TrainData<- | TrainData: set and retrieve training data |
| TrainData<--method | TrainData: set and retrieve training data |
| TrainOptions | TrainOptions: set and retrieve training options |
| TrainOptions-method | TrainOptions: set and retrieve training options |
| TrainOptions<- | TrainOptions: set and retrieve training options |
| TrainOptions<--method | TrainOptions: set and retrieve training options |
| TrainStats | TrainStats: set and retrieve training statistcs |
| TrainStats-method | TrainStats: set and retrieve training statistcs |
| TrainStats<- | TrainStats: set and retrieve training statistcs |
| TrainStats<--method | TrainStats: set and retrieve training statistcs |
| viewNames | viewNames: set and retrieve view names |
| viewNames-method | viewNames: set and retrieve view names |
| viewNames<- | viewNames: set and retrieve view names |
| viewNames<--method | viewNames: set and retrieve view names |