# Generating Multi-Omics Datasets for Testing and Benchmarking

## Documentation for package ‘SUMO’ version 1.2.2

- 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)