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Simulate Shared + Specific Multi-Omics Data via InterSIM

Source: R/sim_intersim_shared_specific.R
simulate_intersim_shared_specific.Rd

Generate multi-omics data where shared signal is provided by InterSIM::InterSIM() and additional omics-specific signal is injected by per-omics latent labels U.

Usage

simulate_intersim_shared_specific(
  n = 500,
  Z_prop = c(0.3, 0.3, 0.4),
  delta_methyl = 2,
  delta_expr = 2,
  delta_protein = 2,
  p_DMP = 0.2,
  p_DEG = NULL,
  p_DEP = NULL,
  p_spec_feat = 0.05,
  delta_spec = c(methyl = 1, gene = 1, protein = 1),
  U_nclass = 2,
  U_within_Z = TRUE,
  max_features_per_block = 400,
  sample_prefix = "S",
  return_workflow_data = TRUE,
  keep_sim_raw = TRUE,
  seed = NULL
)

Arguments

n

Number of samples.

Z_prop

Cluster proportion for InterSIM shared clusters.

delta_methyl

Shared-signal strength for methylation in InterSIM.

delta_expr

Shared-signal strength for expression in InterSIM.

delta_protein

Shared-signal strength for protein in InterSIM.

p_DMP

Proportion of differential methylation features in InterSIM. Default matches InterSIM::InterSIM() (0.2).

p_DEG

Proportion of differential expression features in InterSIM. Default matches InterSIM::InterSIM() (NULL).

p_DEP

Proportion of differential protein features in InterSIM. Default matches InterSIM::InterSIM() (NULL).

p_spec_feat

Proportion of features used as specific set T per omics.

delta_spec

Named numeric vector with specific shift size for methyl, gene, and protein.

U_nclass

Number of categories for each specific latent label U.

U_within_Z

Logical; whether each U is generated within each shared cluster Z (recommended).

max_features_per_block

Maximum number of features kept per omics block in returned dat.list when return_workflow_data = TRUE.

sample_prefix

Prefix for generated sample IDs in dat.list.

return_workflow_data

Logical; whether to return workflow-ready dat.list, truth, and k_ref.

keep_sim_raw

Logical; whether to keep original InterSIM output as sim_raw.

seed

Optional random seed. If NULL, current RNG state is used.

Value

A list containing:

  • X_list: simulated matrices (methyl, gene, protein)

  • Z: shared labels from InterSIM

  • U: specific labels per omics

  • S: shared feature index sets per omics

  • T: specific feature index sets per omics

  • sim_raw: raw InterSIM output (optional)

  • dat.list, truth, k_ref: workflow-ready outputs (optional)

Details

This function wraps the notebook simulation workflow into a reusable package API and optionally returns workflow-ready dat.list and truth labels.