mclusterSim: Similarity score between clusters of genes based on pathways...
In BioCor: Functional similarities

Description Usage Arguments Value Methods (by class) Author(s) See Also Examples

Looks for the similarity between genes in groups. Once the pathways for each cluster are found they are combined using codecombineScores.

mclusterSim(clusters, info, method = "max", ...)

## S4 method for signature 'list,GeneSetCollection'
mclusterSim(clusters, info, method = "max", ...)

`clusters`	A list of clusters of genes to be found in `id`.
`info`	A GeneSetCollection or a list of genes and the pathways they are involved.
`method`	one of `c("avg", "max", "rcmax", "rcmax.avg", "BMA", "reciprocal")`, see Details.
`...`	Other arguments passed to `combineScores`

mclusterSim returns a matrix with the similarity scores for each cluster comparison.

clusters = list,info = GeneSetCollection: Calculates all the similarities of the GeneSetCollection and combine them using combineScoresPar

Llu<c3><ad>s Revilla

For a different approach see clusterGeneSim, combineScores and conversions

if (require("org.Hs.eg.db")) {
    #Extract the paths of all genes of org.Hs.eg.db from KEGG (last update in
    # data of June 31st 2011)
    genes.kegg <- as.list(org.Hs.egPATH)

    clusters <- list(cluster1 = c("18", "81", "10"),
                     cluster2 = c("100", "10", "1"),
                     cluster3 = c("18", "10", "83"))
    mclusterSim(clusters, genes.kegg)
    mclusterSim(clusters, genes.kegg, "avg")
} else {
    warning('You need org.Hs.eg.db package for this example')
}