R/random_network.r

In leiming8886/fRNC: ncRNA module search functions

random_network <- function (size, G, lambda) 
{
    calculate_score <- function(g) {
        if (ecount(g) > 0) 
            subsum <- (1 - lambda) * sum(V(g)$weight)/sqrt(vcount(g)) + 
                lambda * sum(as.numeric(E(g)$weight))/sqrt(ecount(g))
        else subsum <- (1 - lambda) * sum(V(g)$weight)/sqrt(vcount(g))
        subsum
    }
    genes.idx <- V(G)$name
    l.zperm <- c()
    while (length(l.zperm) < 10000) {
        seed <- sample(genes.idx, 1)
        while (length(seed) < size) {
            tmp.neigh <- V(G)[unlist(neighborhood(G, 1, seed))]$name
            tmp.neigh <- setdiff(tmp.neigh, seed)
            if (length(tmp.neigh) > 0) 
                seed <- c(seed, sample(tmp.neigh, 1))
            else break
        }
        if (length(seed) == size) 
            l.zperm <- c(l.zperm, calculate_score(induced.subgraph(G, 
                seed)))
    }
    l.zperm
}