set_covariates: Add covariates to a MOFA model

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Add covariates to a MOFA model

Description

Function to add continuous covariate(s) to a MOFA object for training with MEFISTO

Usage

set_covariates(object, covariates)

Arguments

object	an untrained MOFA
covariates	Sample-covariates to be passed to the model. This can be either: a character, specifying columns already present in the samples_metadata of the object a data.frame with columns "sample", "covariate", "value". Sample names need to match those present in the data a matrix with smaples in columns and covariate(s) in row(s) Note that the covariate should be numeric and continuous.

Details

To activate the functional MEFISTO framework, specify mefisto_options when preparing the training using prepare_mofa

Value

Returns an untrained MOFA with covariates filled in the corresponding slots

Examples

#' # Simulate data
dd <- make_example_data(sample_cov = seq(0,1,length.out = 100), n_samples = 100, n_factors = 4)

# Create MOFA object
sm <- create_mofa(data = dd$data)

# Add a covariate
sm <- set_covariates(sm, covariates = dd$sample_cov)
sm

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