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# function borrowed from package 'nem', since the installation of
# nem from bioconductor proved problematic
#
transitive.reduction <- function (g)
{
# if (!(class(g) %in% c("matrix", "graphNEL")))
# stop("Input must be an adjacency matrix or graphNEL object")
# if (class(g) == "graphNEL") {
# g = as(g, "matrix")
# }
g = transitive.closure(g, mat = TRUE)
g = g - diag(diag(g))
type = (g > 1) * 1 - (g < 0) * 1
for (y in 1:nrow(g)) {
for (x in 1:nrow(g)) {
if (g[x, y] != 0) {
for (j in 1:nrow(g)) {
if ((g[y, j] != 0) & sign(type[x, j]) * sign(type[x,
y]) * sign(type[y, j]) != -1) {
g[x, j] = 0
}
}
}
}
}
g
}
transitive.closure <- function (g, mat = FALSE, loops = TRUE)
{
# if (!(class(g) %in% c("graphNEL", "matrix")))
# stop("Input must be either graphNEL object or adjacency matrix")
# g <- as(g, "matrix")
n <- ncol(g)
matExpIterativ <- function(x, pow, y = x, z = x, i = 1) {
while (i < pow) {
z <- z %*% x
y <- y + z
i <- i + 1
}
return(y)
}
h <- matExpIterativ(g, n)
h <- (h > 0) * 1
dimnames(h) <- dimnames(g)
if (!loops)
diag(h) <- rep(0, n)
else diag(h) <- rep(1, n)
# if (!mat)
# h <- as(h, "graphNEL")
return(h)
}
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