mclusterGeneSim {BioCor} | R Documentation |
Looks for the similarity between genes of a group and then between each group's genes.
mclusterGeneSim(clusters, info, method = c("max", "rcmax.avg"), ...) ## S4 method for signature 'list,GeneSetCollection' mclusterGeneSim(clusters, info, method = c("max", "rcmax.avg"), ...)
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 |
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 |
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
clusterGeneSim
, clusterSim
and
combineScores
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') }