run_mofa {MOFA2} | R Documentation

## Train a MOFA model

### Description

Function to train an untrained `MOFA` object.

### Usage

    run_mofa(object, outfile = NULL, save_data = TRUE, use_basilisk = FALSE)

### Arguments

`object` | an untrained `MOFA` object
`outfile` | output file for the model (.hdf5 format). If `NULL`, a temporary file is created.
`save_data` | logical indicating whether to save the training data in the hdf5 file. This is useful for some downstream analysis (mainly functions with the prefix `plot_data`), but it can take a lot of disk space.
`use_basilisk` | use `basilisk` to automatically install a conda environment with mofapy2 and all dependencies? If `FALSE` (default), you should specify the right python binary when loading R with `reticulate::use_python(..., force=TRUE)` or the right conda environment with `reticulate::use_condaenv(..., force=TRUE)`.

### Details

This function is called once a MOFA object has been prepared (using `prepare_mofa`) In this step the R package calls the `mofapy2` Python package, where model training is performed.
The interface with Python is done with the `reticulate` package. If you have several versions of Python installed and R is not detecting the correct one, you can change it using `reticulate::use_python` when loading the R session. Alternatively, you can let us install mofapy2 for you using `basilisk` if you set use_basilisk to `TRUE`

### Value

a trained `MOFA` object

### Examples

    # Load data (in data.frame format)
    file <- system.file("extdata", "test_data.RData", package = "MOFA2")
    load(file)

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

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

    # Run the MOFA model
    ## Not run:  MOFAmodel <- run_mofa(MOFAmodel, use_basilisk = TRUE)

[Package MOFA2 version 1.2.2 Index]