get_default_mefisto_options: Get default options for MEFISTO covariates

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

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)

bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.