apComplex (version 2.38.0)

sortComplexes: Sort complex estimates

Description

Sorts complexes recorded in PCMG list into three separate lists containing MBME, SBMH, and UnRBB complexes.

Usage

sortComplexes(PCMG, adjMat)

Arguments

PCMG

Current PCMG estimate

adjMat

Adjacency matrix of bait-hit data from an AP-MS experiment. Rows correspond to baits and columns to hits.

Value

A list of lists representing the MBME, SBMH, and UnRBB complex estimates.

Details

MBME complexes contain multiple bait proteins and multiple edges. SBMH complexes contain one bait and a collection of hit-only proteins. UnRBB complexes contain only two baits (no hit-only proteins) that are connected by an unreciprocated edge.

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

findComplexes

Examples

data(apEX)
PCMG2 <- findComplexes(apEX,sensitivity=.7,specificity=.75)
sortComplexes(PCMG2,apEX)