Nothing
getCZ = function(tree) {
k = (nrow(tree$edge) + 2)/2
t = nrow(tree$cna)
CZ = matrix(nrow = t, ncol = k, data = 0)
rownames(CZ) = rownames(tree$cna)
colnames(CZ) = paste("clone", 1:k, sep = "")
clonal.cna = vector("list", k)
for (tip in 2:k) {
child.node = tip
parent.node = tree$edge[which(tree$edge[, 2] == child.node),
1]
while (parent.node >= (k + 1)) {
cnatemp = intersect(which(tree$cna[, 2] == parent.node),
which(tree$cna[, 3] == child.node))
if (length(cnatemp) > 0) {
clonal.cna[[tip]] = c(clonal.cna[[tip]], cnatemp)
}
child.node = parent.node
if (child.node == (k + 1))
break
parent.node = tree$edge[which(tree$edge[, 2] == child.node),
1]
}
}
clonal.cna[[1]] = 0
for (k in 2:k) {
for (t in 1:t) {
if (is.element(t, clonal.cna[[k]])) {
CZ[t, k] = 1
}
}
}
return(CZ)
}
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