clusterSim: Similarity score between clusters of genes based on pathways...

In llrs/BioCor: Functional similarities

Similarity score between clusters of genes based on pathways similarity

Description

Looks for the similarity between genes in groups

Usage

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

## S4 method for signature '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

Details

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

Value

clusterSim returns a similarity score of the two clusters

Methods (by class)

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

Author(s)

Lluís Revilla

See Also

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

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")
}

llrs/BioCor documentation built on April 24, 2024, 5:50 p.m.