Similarity score between clusters of genes based on pathways similarity
Source:R/mclusterSim.R
mclusterSim.Rd
Looks for the similarity between genes in groups. Once the pathways for each cluster are found they are combined using codecombineScores.
Usage
mclusterSim(clusters, info, method = "max", ...)
# S4 method for class 'list,GeneSetCollection'
mclusterSim(clusters, info, method = "max", ...)
Methods (by class)
mclusterSim(clusters = list, info = GeneSetCollection)
: Calculates all the similarities of the GeneSetCollection and combine them usingcombineScoresPar()
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)
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")
}
#> cluster1 cluster2 cluster3
#> cluster1 0.11837329 0.07739749 0.1158909
#> cluster2 0.07739749 0.26653339 0.1448643
#> cluster3 0.11589087 0.14486431 0.2183986