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

clusterGeneSim(cluster1, cluster2, info, method = c("max", "rcmax.avg"), ...)

# S4 method for class 'character,character,GeneSetCollection'
clusterGeneSim(cluster1, cluster2, info, method = c("max", "rcmax.avg"), ...)

Arguments

cluster1, cluster2: A vector with genes.
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 similarity score between the genes of the two clusters.

Details

Differs with clusterSim that first each combination between genes is calculated, and with this values then the comparison between the two clusters is done. Thus applying combineScores twice, one at gene level and another one at cluster level.

Methods (by class)

clusterGeneSim( cluster1 = character, cluster2 = character, info = GeneSetCollection ): Calculates the gene similarities in a GeneSetCollection and combine them using combineScoresPar()

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)
    clusterGeneSim(c("18", "81", "10"), c("100", "10", "1"), genes.kegg)
    clusterGeneSim(
        c("18", "81", "10"), c("100", "10", "1"), genes.kegg,
        c("avg", "avg")
    )
    clusterGeneSim(
        c("18", "81", "10"), c("100", "10", "1"), genes.kegg,
        c("avg", "rcmax.avg")
    )
    (clus <- clusterGeneSim(
        c("18", "81", "10"), c("100", "10", "1"),
        genes.kegg, "avg"
    ))
    combineScores(clus, "rcmax.avg")
} else {
    warning("You need org.Hs.eg.db package for this example")
}
#> Loading required package: org.Hs.eg.db
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