Generate synthetic GeneWalk data

Generates a synthetic network that mimics real GeneWalk input data for testing and benchmarking. The network consists of three components: a hierarchical ontology (tree structure with lateral edges), gene-to-ontology annotations, and protein-protein interactions (PPI).

Signal genes are annotated exclusively within a single ontology subtree and form PPI edges among themselves, creating coherent graph neighbourhoods. Noise genes receive the same number of annotations but are forced to span multiple subtrees, and their PPI edges are random across the noise group. Both groups are degree-matched so that significance is driven by annotation coherence rather than connectivity alone.

Usage

synthetic_genewalk_data(data_params = params_genewalk_data(), seed = 42L)

Arguments

data_params

Named list. Return from params_genewalk_data().

seed

Integer. Random seed. Defaults to 42L.

Value

A list with the following items:

full_data

A data.table with columns from and to containing all edges (ontology hierarchy, gene-to-pathway, and PPI).

gene_to_pathways

A data.table with columns from (gene) and to (pathway) for gene-to-ontology annotation edges only.

gene_ids

Character vector of all gene identifiers (signal and noise).

pathway_ids

Character vector of all ontology term identifiers.