prepare_mofa {MOFA2} | R Documentation

## Prepare a MOFA for training

### Description

Function to prepare a `MOFA` object for training. It requires defining data, model and training options.

### Usage

    prepare_mofa(
      object,
      data_options = NULL,
      model_options = NULL,
      training_options = NULL,
      stochastic_options = NULL,
      mefisto_options = NULL
    )

### Arguments

`object` | an untrained `MOFA`
`data_options` | list of data_options (see `get_default_data_options` details). If NULL, default options are used.
`model_options` | list of model options (see `get_default_model_options` for details). If NULL, default options are used.
`training_options` | list of training options (see `get_default_training_options` for details). If NULL, default options are used.
`stochastic_options` | list of options for stochastic variational inference (see `get_default_stochastic_options` for details). If NULL, default options are used.
`mefisto_options` | list of options for mefisto (see `get_default_mefisto_options` for details). If NULL, default options are used.

### Details

This function is called after creating a `MOFA` object (using `create_mofa`) and before starting the training (using `run_mofa`). Here, we can specify different options for the data (data_options), the model (model_options) and the trainig (training_options, stochastic_options). Take a look at the individual default options for an overview using the get_default_XXX_options functions above.

### Value

Returns an untrained `MOFA` with specified options filled in the corresponding slots

### Examples

    # Using an existing simulated data with two groups and two views
    file <- system.file("extdata", "test_data.RData", package = "MOFA2")

    # Load data dt (in data.frame format)
    load(file)

    # Create the MOFA object
    MOFAmodel <- create_mofa(dt)

    # Prepare MOFA object using default options
    MOFAmodel <- prepare_mofa(MOFAmodel)

    # Prepare MOFA object changing some of the default model options values
    model_opts <- get_default_model_options(MOFAmodel)
    model_opts$num_factors <- 10
    MOFAmodel <- prepare_mofa(MOFAmodel, model_options = model_opts)

[Package MOFA2 version 1.4.0 Index]