simulate_twoOmicsData()
multiomics_demo = "SHOW" provides a ready-to-run two-factor toy example for quick multi-omics walkthroughs.Legacy → standard conversion pipeline
Polished as_multiomics() to reliably upgrade legacy simulate_twoOmicsData() outputs into the current schema (omics, per-omic list_betas, signal_annotation$features, factor_map, etc.), including:
alpha{n}),delta{n} → beta{n} for omic 2,concatenated_datasets back into omic1/omic2 using counts or omic1_/omic2_ prefixes.Internal helpers made non-exported (with docs scaffolding)
%||% for defaults and .is_multiomics_like() for schema checks are now internal, with roxygen headers (no code changes).
Stronger standardization & resilience
Automatic row/column naming for omics matrices; safer handling of empty/NA index vectors; improved messages for sample-partition constraints; sturdier concatenated-split heuristics.
as_multiomics(), and configuring basilisk/reticulate backends.delta→beta mapping across omics.as_multiomics() to standardize them for downstream workflows.