Similarity score between clusters of genes based on pathways similarity

Looks for the similarity between genes in groups

Usage

clusterSim(cluster1, cluster2, info, method = "max", ...)

# S4 method for character,character,GeneSetCollection
clusterSim(cluster1, cluster2, info, method = "max", ...)

Arguments

cluster1, cluster2

A vector with genes.

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

Value

clusterSim returns a similarity score of the two clusters

Details

Once the pathways for each cluster are found they are combined using combineScores().

Methods (by class)

• clusterSim( cluster1 = character, cluster2 = character, info = GeneSetCollection ): Calculates all the similarities of the GeneSetCollection and combine them using combineScoresPar()

See also

For a different approach see clusterGeneSim(), combineScores() and conversions()

Author

Lluís Revilla

Examples

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)
    clusterSim(c("9", "15", "10"), c("33", "19", "20"), genes.kegg)
    clusterSim(c("9", "15", "10"), c("33", "19", "20"), genes.kegg, NULL)
    clusterSim(c("9", "15", "10"), c("33", "19", "20"), genes.kegg, "avg")
} else {
    warning("You need org.Hs.eg.db package for this example")
}
#> [1] 0.07083146