get_default_mefisto_options {MOFA2} | R Documentation

## Get default options for MEFISTO covariates

### Description

Function to obtain the default options for the usage of MEFISTO covariates with MEFISTO

### Usage

    get_default_mefisto_options(object)

### Arguments

`object` | an untrained `MOFA` object

### Details

The options are the following:

- scale_cov: logical: Scale covariates?

- start_opt: integer: First iteration to start the optimisation of GP hyperparameters

- n_grid: integer: Number of points for the grid search in the optimisation of GP hyperparameters

- opt_freq: integer: Frequency of optimisation of GP hyperparameters

- sparseGP: logical: Use sparse GPs to speed up the optimisation of the GP parameters?

- frac_inducing: numeric between 0 and 1: Fraction of samples to use as inducing points (only relevant if sparseGP is `TRUE`)

- warping: logical: Activate warping functionality to align covariates between groups (requires a multi-group design)

- warping_freq: numeric: frequency of the warping (only relevant if warping is `TRUE`)

- warping_ref: A character specifying the reference group for warping (only relevant if warping is `TRUE`)

- warping_open_begin: logical: Warping: Allow for open beginning? (only relevant warping is `TRUE`)

- warping_open_end: logical: Warping: Allow for open end? (only relevant warping is `TRUE`)

- warping_groups: Assignment of groups to classes used for alignment (advanced option). Needs to be a vector of length number of samples, e.g. a column of samples_metadata, which needs to have the same value within each group. By default groups are used specified in 'create_mofa'.

- model_groups: logical: Model covariance structure across groups (for more than one group, otherwise FALSE)? If FALSE, we assume the same patterns in all groups.

- new_values: Values for which to predict the factor values (for interpolation / extrapolation). This should be numeric matrix in the same format with covariate(s) in rows and new values in columns. Default is NULL, leading to no interpolation.

### Value

Returns a list with default options for the MEFISTO covariate(s) functionality.

### Examples

    # generate example data
    dd <- make_example_data(sample_cov = seq(0,1,length.out = 200), n_samples = 200,
    n_factors = 4, n_features = 200, n_views = 4, lscales = c(0.5, 0.2, 0, 0))
    # input data
    data <- dd$data
    # covariate matrix with samples in columns
    time <- dd$sample_cov
    rownames(time) <- "time"

    # create mofa and set covariates
    sm <- create_mofa(data = dd$data)
    sm <- set_covariates(sm, covariates = time)

    MEFISTO_opt <- get_default_mefisto_options(sm)

[Package MOFA2 version 1.4.0 Index]