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

Description Usage Arguments Value Methods (by class) Author(s) See Also Examples

View source: R/mclusterSim.R

Description

Looks for the similarity between genes in groups. Once the pathways for each cluster are found they are combined using codecombineScores.

Usage

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mclusterSim(clusters, info, method = "max", ...)

## S4 method for signature 'list,GeneSetCollection'
mclusterSim(clusters, info,
  method = "max", ...)

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

one of c("avg", "max", "rcmax", "rcmax.avg", "BMA", "reciprocal"), see Details.

...

Other arguments passed to combineScores

Value

mclusterSim returns a matrix with the similarity scores for each cluster comparison.

Methods (by class)

Author(s)

Lluís Revilla

See Also

For a different approach see clusterGeneSim, combineScores and conversions

Examples

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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)

    clusters <- list(cluster1 = c("18", "81", "10"),
                     cluster2 = c("100", "10", "1"),
                     cluster3 = c("18", "10", "83"))
    mclusterSim(clusters, genes.kegg)
    mclusterSim(clusters, genes.kegg, "avg")
} else {
    warning('You need org.Hs.eg.db package for this example')
}

BioCor documentation built on Nov. 1, 2018, 3:34 a.m.