Similarity score between clusters of genes based on genes similarity

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

Usage

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

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

Arguments

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

Value

Returns a matrix with the similarity scores for each cluster comparison.

Methods (by class)

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

See also

clusterGeneSim(), clusterSim() and combineScores()

Author

Lluís Revilla

Examples

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")
}
#>           cluster1  cluster2  cluster3
#> cluster1 1.0000000 1.0000000 0.8022654
#> cluster2 1.0000000 1.0000000 0.8304646
#> cluster3 0.8022654 0.8304646 1.0000000