ibhClusterEvalBioGRID: Evaluate clustering with interaction based homogeneity using...

In ibh: Interaction Based Homogeneity for Evaluating Gene Lists

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

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

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")

ibh documentation built on Nov. 8, 2020, 7:49 p.m.