Nothing
getKmeans <- function(sam.dat,iter.max=10,para){
# BAF data are first normalized so that it has the same range as logR
# a threshold is set to grasp the first best-fit kmeans center numbers
# this threshold is normalized by logR range
thr<-para$thr.kmeans
dat.norm <- (range(sam.dat[,4])[2]-range(sam.dat[,4])[1])/(range(sam.dat[,6])[2]-range(sam.dat[,6])[1])
thr.norm <- thr*dat.norm
BAF<-sam.dat[,6]*dat.norm
logR<-sam.dat[,4]
ncenters <- 2
while(1){
cl <- kmeans(cbind(BAF,logR),iter.max=iter.max,centers=ncenters,nstart=50)
tag <- 0
for(i in cl$withinss){
if(i >= thr.norm){
tag<-1
break
}
}
if(tag==0){
break
}
ncenters <- ncenters+1
}
cl$centers[,1]<-cl$centers[,1]/dat.norm
return(cl)
}
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