MOFAmodel {MOFA} | R Documentation

## Class to store a Multi-Omics Factor Analysis (MOFA) model

### Description

The `MOFAmodel` is an S4 class used to store all relevant data to analyse a MOFA model.

### Slots

`InputData`

  the input data before being parsed to Training Data. Either a MultiAssayExperiment object or a list of matrices, one per view.

`TrainData`

  the parsed data used to fit the MOFA model A list with one matrix per view.

`ImputedData`

  the parsed data with the missing values imputed using the MOFA model. A list with one matrix per view.

`Expectations`

  expected values of the different variables of the model. A list of matrices, one per variable. The most relevant are "W" for weights and "Z" for factors.

`TrainStats`

  list with training statistics such as evidence lower bound (ELBO), number of active factors, etc.

`DataOptions`

  list with the data processing options such as whether to center or scale the data.

`TrainOptions`

  list with the training options such as maximum number of iterations, tolerance for convergence, etc.

`ModelOptions`

  list with the model options such as likelihoods, number of factors, etc.

`FeatureIntercepts`

  list with the feature-wise intercepts. Only used internally.

`Dimensions`

  list with the relevant dimensionalities of the model. N for the number of samples, M for the number of views, D for the number of features of each view and K for the number of infered latent factors.

`Status`

  Auxiliary variable indicating whether the model has been trained.

[Package MOFA version 1.0.0 Index]