make_example_data: Simulate a data set using the generative model of MOFA

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Simulate a data set using the generative model of MOFA

Description

Function to simulate an example multi-view multi-group data set according to the generative model of MOFA2.

Usage

make_example_data(
  n_views = 3,
  n_features = 100,
  n_samples = 50,
  n_groups = 1,
  n_factors = 5,
  likelihood = "gaussian",
  lscales = 1,
  sample_cov = NULL,
  as.data.frame = FALSE
)

Arguments

n_views	number of views
n_features	number of features in each view
n_samples	number of samples in each group
n_groups	number of groups
n_factors	number of factors
likelihood	likelihood for each view, one of "gaussian" (default), "bernoulli", "poisson", or a character vector of length n_views
lscales	vector of lengthscales, needs to be of length n_factors (default is 0 - no smooth factors)
sample_cov	(only for use with MEFISTO) matrix of sample covariates for one group with covariates in rows and samples in columns or "equidistant" for sequential ordering, default is NULL (no smooth factors)
as.data.frame	return data and covariates as long dataframe

Value

Returns a list containing the simulated data and simulation parameters.

Examples

# Generate a simulated data set
MOFAexample <- make_example_data()

bioFAM/MOFA2 documentation built on Feb. 1, 2024, 6:41 a.m.