apComplex (version 2.38.0)

bhmaxSubgraph: Find maximal BH-complete subgraph

Description

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.

Usage

bhmaxSubgraph(adjMat,VBs=NULL,VPs=NULL,unrecip=1)

Arguments

adjMat

adjMat is an N by (N+M) adjacency matrix with N equal to the number of bait proteins and M equal to the number of hit-only proteins. adjMat should have row and column names corresponding to the proteins in the experiment. An entry of "1" in the ith row and jth column of adjMat corresponds to bait protein i finding protein j as a hit. All other entries should be 0.

VBs

VBs is an optional vector of viable baits.

VPs

VPs is an optional vector of viable prey.

unrecip

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.

Value

A list of length one named 'maxCliques' which is itself a list of character vectors containing the names of the elements in the cliques.

Details

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.

If VBs and/or VPs are not specified, then by default VBs will be assigned the set of baits that detect at least one prey and VPs 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 unrecip=1.

This function calls maxCliques from the RBGL package.

References

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).

See Also

mergeComplexes,findComplexes

Examples

data(apEX)
PCMG0 <- bhmaxSubgraph(apEX)
PCMG1 <- mergeComplexes(PCMG0,apEX,sensitivity=.7,specificity=.75)