evaluateClustering {GOSim}R Documentation

Evaluate a given grouping of genes or GO terms.

Description

Evaluate a given grouping of genes or terms with respect to their GO similarity.

Usage

evaluateClustering(clust, Sim)

Arguments

clust grouping = vector of integer or character
Sim similarity matrix

Details

If necessary, more details than the description above

Value

List with two items:

clusterstats matrix (ncluster x 2) of median within cluster similarities and median absolute deviations
clustersil cluster silhouette values

Author(s)

Holger Froehlich

References

Rousseeuw, P., Silhouettes: a graphical aid to the interpretation and validation of cluster analysis, J. Comp. and Applied Mathematics, 1987, 20, 53-6

See Also

getGeneSimPrototypes, getGeneSim, getTermSim

Examples

        ## Not run: 
        setOntology("BP")
        genes = c("207","208","596","901","780","3169","9518","2852","26353","8614","7494")
        sim = getGeneSim(genes,verbose=FALSE)
        ev = evaluateClustering(c(2,3,2,3,1,2,1,1,3,1,2), sim)
        print(ev$clusterstats)
        plot(ev$clustersil,main="")
        
## End(Not run)

[Package GOSim version 1.0.2 Index]