evaluateClustering {GOSim} | R Documentation |
Evaluate a given grouping of genes or terms with respect to their GO similarity.
evaluateClustering(clust, Sim)
clust |
grouping = vector of integer or character |
Sim |
similarity matrix |
If necessary, more details than the description above
List with two items:
clusterstats |
matrix (ncluster x 2) of median within cluster similarities and median absolute deviations |
clustersil |
cluster silhouette values |
Holger Froehlich
Rousseeuw, P., Silhouettes: a graphical aid to the interpretation and validation of cluster analysis, J. Comp. and Applied Mathematics, 1987, 20, 53-6
getGeneSimPrototypes
, getGeneSim
, getTermSim
## 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)