Nothing
getZ = function(tree, sna.name) {
k = (nrow(tree$edge) + 2)/2
s = nrow(tree$sna)
Z = matrix(nrow = s, ncol = k, data = 0)
rownames(Z) = sna.name
colnames(Z) = paste("clone", 1:k, sep = "")
clonal.sna = vector("list", k)
for (tip in 2:k) {
child.node = tip
parent.node = tree$edge[which(tree$edge[, 2] == child.node), 1]
while (parent.node >= (k + 1)) {
snatemp = intersect(which(tree$sna[, 2] == parent.node),
which(tree$sna[, 3] == child.node))
if (length(snatemp) > 0) {
clonal.sna[[tip]] = c(clonal.sna[[tip]], snatemp)
}
child.node = parent.node
if (child.node == (k + 1))
break
parent.node = tree$edge[which(tree$edge[, 2] == child.node), 1]
}
}
clonal.sna[[1]] = 0
for (ki in 2:k) {
Z[clonal.sna[[ki]],ki]=1
}
return(Z)
}
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