get_default_data_options: Get default data options

In MOFA2: Multi-Omics Factor Analysis v2

Description

Function to obtain the default data options.

Usage

get_default_data_options(object)

Arguments

object

an untrained MOFA object

Details

This function provides a default set of data options that can be modified and passed to the MOFA object in the prepare_mofa step (see example), i.e. after creating a MOFA object (using create_mofa) and before starting the training (using run_mofa) The data options are the following:

• scale_views: logical indicating whether to scale views to have the same unit variance. As long as the scale differences between the views is not too high, this is not required. Default is FALSE.

• scale_groups: logical indicating whether to scale groups to have the same unit variance. As long as the scale differences between the groups is not too high, this is not required. Default is FALSE.

Value

Returns a list with the default data options.

Examples

# Using an existing simulated data with two groups and two views
file <- system.file("extdata", "test_data.RData", package = "MOFA2")

# Load data dt (in data.frame format)
load(file) 

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

# Load default data options
data_opts <- get_default_data_options(MOFAmodel)

# Edit some of the data options
data_opts$scale_views <- TRUE

# Prepare the MOFA object
MOFAmodel <- prepare_mofa(MOFAmodel, data_options = data_opts)

MOFA2 documentation built on Nov. 8, 2020, 7:28 p.m.