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 |