Generating Multi-Omics Datasets for Testing and Benchmarking

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Documentation for package ‘SUMO’ version 1.2.3

• DESCRIPTION file.
• Package NEWS.

Help Pages

SUMO-package	SUMO: Simulation Utilities for Multi-Omics Data
as_multiomics	Convert legacy objects (e.g., from 'simulate_twoOmicsData()') to the current standardized structure used by downstream tools.
compute_means_vars	Compute Summary Statistics for a List of Datasets
demo_multiomics_analysis	Demonstration of SUMO Utility in Multi-Omics Analysis using MOFA2
divide_features_one	Dividing features to create vectors with signal in the first omic for single data
divide_features_two	Dividing features to create vectors with signal in the second omic for single data
divide_samples	Global Variable
divide_vector	#' Global Variable #' #' A global variable used in multiple functions. #' #'
feature_selection_one	Dividing features to create vectors with signal in the first omic
feature_selection_two	Dividing features to create vectors with signal in the second omic
plot_factor	Visualization of factor scores (ground truth)
plot_simData	Visualize simulated multi-omics data as a heatmap
plot_weights	Visualize feature loadings (weights)
simulateMultiOmics	Simulation of omics with predefined single or multiple latent factors in multi-omics
simulate_twoOmicsData	Simulation of omics with predefined single or multiple latent factors in multi-omics
SUMO	SUMO: Simulation Utilities for Multi-Omics Data
sumo_load_pretrained_mofa	Load a pretrained MOFA model (no Python required)
sumo_pretrained_mofa_available	List pretrained MOFA models included with SUMO
sumo_pretrained_mofa_path	Path to a pretrained MOFA model shipped with SUMO
sumo_setup_mofa	Interactive setup for Python 'mofapy2' via reticulate (fallback when basilisk is unavailable)