Given an adjacency matrix of bait-hit AP-MS protein data, this function finds the maximal BH-complete subgraphs and reports them as an affiliation matrix.
By default set to 1 so that unreciprocated bait-bait edges are treated as present. If set to 0, unreciprocated bait-bait edges will be treated as absent.
A BH-complete subgraph with n bait nodes and m hit-only nodes for AP-MS data is defined as a subgraph for which all n*(n-1)+nm directed edges exist. A maximal BH-complete subgraph is a BH-complete subgraph which is not contained in any other BH-complete subgraph.
VPs are not specified, then by default
will be assigned the set of baits that detect at least one prey and
the set of prey that are detected by at least one bait.
By default, unreciprocated bait-bait observations will be
treated as present. If
unrecip is set to 0, they will be treated as
absent. If the sensitivity of the AP-MS technology is believed to be less
than the specificity, then it is suggested that
This function calls
maxCliques from the RBGL package.
A list of length one named 'maxCliques' which is itself a list of character vectors containing the names of the elements in the cliques.
Scholtens D and Gentleman R. Making sense of high-throughput protein-protein interaction data. Statistical Applications in Genetics and Molecular Biology 3, Article 39 (2004).
Scholtens D, Vidal M, and Gentleman R. Local modeling of global interactome networks. Bioinformatics 21, 3548-3557 (2005).
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