pamfn <-
function(i,p,LS.pam1,data)
{ # run this over the different number of features
thres <- cbind(LS.pam1$threshold, LS.pam1$nonzero, LS.pam1$errors)
thres=thres[(thres[,3]==(min(thres[((thres[,2]<=p[i]*3/2+20)&(thres[,2]>=p[i])),3])))&(thres[,2]<=p[i]*3/2+20)&(thres[,2]>=p[i]),1] # use ALL criterias to identify diff thresholds
thres=thres[length(thres)] # take the highest threshold
LS.p1=pamr.listgenes(LS.pam1,data=data,threshold=thres) # pam centroids...genes are ranked by importance
LS.p1=cbind(as.double(LS.p1[,1]),abs(as.double(LS.p1[,2])))
LS.p1[1:p[i],1]
}
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