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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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