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

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

View source: R/mclusterGeneSim.R

Description

Looks for the similarity between genes of a group and then between each group's genes.

Usage

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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)

Author(s)

Lluís Revilla

See Also

clusterGeneSim, clusterSim and combineScores

Examples

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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')
}

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