mantispy.ds.interactions

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mantispy.ds.interactions#

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

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.

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