###################################################
### chunk number 1: 
###################################################
library(GOSemSim)
goSim("GO:0004022", "GO:0005515", ont="MF", measure="Wang")


###################################################
### chunk number 2: 
###################################################
go1 = c("GO:0004022","GO:0004024","GO:0004174")
go2 = c("GO:0009055","GO:0005515")

mgoSim(go1, go2, ont="MF", measure="Wang")


###################################################
### chunk number 3: 
###################################################
geneSim("241", "2561", ont="MF", organism="human", measure="Wang")


###################################################
### chunk number 4: 
###################################################
sim <- mgeneSim(c("835", "5261","241", "934"), ont="MF", organism="human", measure="Wang")
sim

library(cluster)
pamCluster <- pam(as.dist(1-sim[complete.cases(sim), complete.cases(sim)]), 2)
pamCluster$clustering


###################################################
### chunk number 5: 
###################################################
cluster1 <- c("snR67","snR40","snR48", "snR17a","snR8")
cluster2 <- c("YOR251C", "YPR137C-B", "YPR010C", "YPR072W")
cluster3 <- c("YNL133C", "YOL041C", "YOL018C", "YOR236W",  "YOR179C", "YOR230W")
clusterSim(cluster1, cluster2, ont="MF", organism="yeast", measure="Wang")
clusters <- list(a=cluster1, b=cluster2, c=cluster3)
mclusterSim(clusters, ont="MF", organism="yeast", measure="Wang")