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

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

Looks for the similarity between genes of a group and then between each group's genes.

mclusterGeneSim(clusters, info, method = c("max", "rcmax.avg"), ...)

## S4 method for signature 'list,GeneSetCollection'
mclusterGeneSim(clusters, info, method = c("max", "rcmax.avg"), ...)

`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`	A vector with two or one argument to be passed to combineScores the first one is used to summarize the similarities of genes, the second one for clusters.
`...`	Other arguments passed to `combineScores`

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

clusterGeneSim, clusterSim and combineScores

if (require("org.Hs.eg.db")) {
    genes.kegg <- as.list(org.Hs.egPATH)
    clusters <- list(cluster1 = c("18", "81", "10"),
                     cluster2 = c("100", "594", "836"),
                     cluster3 = c("18", "10", "83"))
    mclusterGeneSim(clusters, genes.kegg)
    mclusterGeneSim(clusters, genes.kegg, c("max", "avg"))
    mclusterGeneSim(clusters, genes.kegg, c("max", "BMA"))
} else {
    warning('You need org.Hs.eg.db package for this example')
}