Evaluate clustering with interaction based homogeneity using BioGRID Interactions

Description

This function calculated interaction based homogeneity for a clustering result to the BioGRID Interactions for seven organisms: Arabidopsis thaliana(arabidopsis), Caenerhabditis elegans(c.elegans), Drosophila melanogaster (fruitFly), Homo sapiens (human), Mus musculus (mouse), Saccharomyces cerevisae (yeast), Schizosaccharomyces pombe (s.pombe). Unique ids(systematic names), official names or Entrez ids can be used as identifier type.

Usage

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ibhClusterEvalBioGRID(cluster, allGenesList, 
    organism, idType = "EntrezId")

Arguments

cluster

result of clustering

allGenesList

list of genes in the same order of clustering object

organism

organism name, can be one of 'arabidopsis', 'c.elegans', 'fruitFly', 'human', 'mouse', 'yeast', 's.pombe'.

idType

type of identifier, can be one of 'EntrezId', 'Official' and 'UniqueId'.

Value

A vector of floats representing interaction based homogeneity for each cluste

References

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9

Examples

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require(yeastCC)
require(stats)
require(simpIntLists)
data(yeastCC)
subset <- exprs(yeastCC)[1:50,]
d <- dist(subset,method="euclidean")
k <- kmeans(d, 3);
ibhClusterEvalBioGRID(k$cluster, rownames(subset), 
			organism="yeast", idType="UniqueId")