sortComplexes: Sort complex estimates

In apComplex: Estimate protein complex membership using AP-MS protein data

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.

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.

Value

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

Author(s)

Denise Scholtens

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)

apComplex documentation built on Nov. 8, 2020, 7:43 p.m.