mclusterGeneSim: Similarity score between clusters of genes based on genes...

In llrs/BioCor: Functional similarities

Similarity score between clusters of genes based on genes similarity

Description

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 signature '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()

Author(s)

Lluís Revilla

See Also

clusterGeneSim(), clusterSim() and combineScores()

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")
}

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