mclusterSim {BioCor} | R Documentation |
Looks for the similarity between genes in groups. Once the pathways for each cluster are found they are combined using codecombineScores.
mclusterSim(clusters, info, method = "max", ...) ## S4 method for signature 'list,GeneSetCollection' mclusterSim(clusters, info, method = "max", ...)
clusters |
A list of clusters of genes to be found in |
info |
A list or a GeneSetCollection of genes and the pathways they are involved. |
method |
one of |
... |
Other arguments passed to |
mclusterSim
returns a matrix with the similarity scores for
each cluster comparison.
clusters = list,info = GeneSetCollection
: Calculates all the similarities of the GeneSetCollection
and combine them using combineScoresPar
LluĂs Revilla
For a different approach see clusterGeneSim
,
combineScores
and conversions
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') }