yNameTAP: TAP data complex estimates using standard gene names

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

Description

Affiliation matrices with rows corresponding to proteins and columns corresponding to complexes.

Usage

data(yNameTAP)

Details

These are the results from an analysis of the TAP data (Gavin et al., 2002) by Scholtens and Gentleman (2004) and Scholtens, Vidal, and Gentleman (submitted). These estimates were constructed using findComplexes with a sensitivity parameter of .75, specificity of .995, and Beta=-0.2 for externally derived similarity measure based on Gene Ontology cellular component annotation (see Scholtens and Gentleman (2004)).

yNameTAP contains 260 multi-bait-multi-edge complex estimates.

Source

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).

References

Gavin, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).

See Also

TAP, TAPgraph, yTAP, findComplexes

Examples

data(yNameTAP)
yNameTAP[1:10,1:3]

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