mantispy.ds.interactions

mantispy.ds.interactions(source='CORUM', organism='human', cache_dir=None)

Within-complex gene pairs from a complex resource, as an undirected edge list.

Every pair of genes in the same complex becomes one edge, which is the reference network_enrichment() tests the most-similar perturbation pairs against.

Parameters:

source str (default: 'CORUM')

A complex resource gene_sets() can return as source (complex) and target (gene). "CORUM" (the default) uses the packaged CORUM complexes.

organism str (default: 'human')

The organism the resource is fetched for.

cache_dir str | Path | None (default: None)

Where the snapshot is kept. Defaults to mantispy.settings.cache_dir.

Return type:

DataFrame

Returns:

A frame with gene_a and gene_b (gene_a < gene_b), one row per unordered pair of genes that share a complex, deduplicated across complexes.

Notes

The pinned snapshot means the default reference of network_enrichment() is reproducible and needs no network after the first call. For a real protein-protein interaction network, pass a two-column edge frame as edges instead.