SUMO 1.2.0

🧪 Major Simulation Engine Upgrade

• ✅ Support for simulating >2 omics datasets: A core feature upgrade enabling generation of multi-omics datasets with three or more layers, such as transcriptomics, proteomics, and metabolomics, in a single simulation run.

• 🔄 Function renamed for clarity:

  • Previous: OmixCraftHD → Now: simulate_twoOmicsData (for 2-omics simulation).
  • New: OmixCraftMultiHD (alias simulateMultOmics) introduced to simulate an arbitrary number of omics using the same generative framework.

• 💡 Non-overlapping latent factors with flexible per-omic and per-factor signal regions are now seamlessly handled for multiple datasets.

🧬 Factor Model Design Enhancements

• Fully modular generative factor model allows:

  • Signal assignment via latent factors per omic.
  • num.factor = "single" or "multiple" control.
  • factor_structure for each factor: shared, unique, mixed, or partial.

• Sample blocks and feature blocks are now simulated with sequential, non-overlapping indices, respecting biological plausibility and avoiding signal bleed.

🛠️ Refinements and Validation

• Robust input checks ensure valid parameterization for complex simulation designs.
• All alpha (sample score) vectors and beta (feature weight) vectors now support sparse signal encoding and customized signal-to-noise ratios (snr).
• Each omics layer can be assigned its own mean and standard deviation for signal blocks, increasing realism.

📈 Documentation and Usability

• Improved documentation and usage examples for:

  • simulateMultiOmics()
  • Factor assignment logic and feature-sample block allocation

• Example usage includes:

  sim_object <- simulateMultiOmics(
    vector_features = c(3000, 2500, 2000),
    n_samples = 100,
    n_factors = 3,
    snr = 3,
    signal.samples = c(5, 1),
    signal.features = list(c(3, 0.3), c(2.5, 0.25), c(2, 0.2)),
    factor_structure = "mixed",
    num.factor = "multiple",
    seed = 123
  )

📦 Infrastructure

• Full compatibility with Roxygen2, pkgdown, and devtools::check() (0 errors, 0 warnings, 0 notes).
• Added CRAN-safe global variable declarations.