# CMSgenepairs.R
CMSgenepairs=function(Exp)
{
data(pairs)
library(randomForest)
G <- unique(c(pair1[,1],pair1[,2]))
Exp <- missingValue(Exp,G)
coms=(Exp[match(pair1[,1],rownames(Exp)),,drop=F]-Exp[match(pair1[,2],rownames(Exp)),,drop=F])>0
coms=apply(coms,2,function(x) as.numeric(x))
rownames(coms)=paste("pair",1:nrow(coms),sep = "")
res <- as.data.frame(predict(rf, t(coms), type = "prob"))
names(res) <- paste(names(res), ".posteriorProb", sep = "")
res$predictedCMS <- apply(res, 1, function(z) {
y <- which(z == max(z))
paste(c("CMS1", "CMS2", "CMS3", "CMS4")[y], collapse = ",")
})
res
}
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