affinityMatrix <- function(Diff,K=20,sigma=0.5) {
###This function constructs similarity networks.
N = nrow(Diff)
Diff = (Diff + t(Diff)) / 2
diag(Diff) = 0;
sortedColumns = as.matrix(t(apply(Diff,2,sort)))
finiteMean <- function(x) { mean(x[is.finite(x)]) }
means = apply(sortedColumns[,1:K+1],1,finiteMean)+.Machine$double.eps;
avg <- function(x,y) ((x+y)/2)
Sig = outer(means,means,avg)/3*2 + Diff/3 + .Machine$double.eps;
Sig[Sig <= .Machine$double.eps] = .Machine$double.eps
densities = dnorm(Diff,0,sigma*Sig,log = FALSE)
W = (densities + t(densities)) / 2
return(W)
}
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