Nothing

```
netwAttr <-
function(mAPKLObj, net="clr") {
netObj <- new("NetAttr")
mi <- knnmi.all(mAPKLObj@rankedIntens)
if(net=="aracne.a")
grn.net <- aracne.a(mi,0.05)
else if(net=="aracne.m")
grn.net <- aracne.m(mi,0.15)
else
grn.net <- clr(mi)
graph.net <- graph.adjacency(grn.net, weighted=TRUE)
edgelist <- get.edgelist(graph.net)
edgelist <- cbind(edgelist, rep(0, length(edgelist[,1])))
edgelist[,3] <- E(graph.net)$weight ## This object is an output
colnames(edgelist) <- c("#Node1", "Node2", "Weight")
netObj@edgelist <- edgelist
DegreeLocal <- degree(graph.net)
DegreeGlobal <- mean(DegreeLocal)
## weighted degree
WDegreeLocal <- graph.strength(graph.net, weights=edgelist[,3])
WDegreeGlobal <- mean(WDegreeLocal)
netObj@degree <- list(
degreeL = DegreeLocal,
degreeG = DegreeGlobal,
WdegreeL = round(WDegreeLocal, 2),
WdegreeG = WDegreeGlobal
)
WClosenessLocal <- closeness(graph.net, weights=edgelist[,3])
WClosenessGlobal <- mean(WClosenessLocal)
netObj@closeness <- list(
WclosenessL = round(WClosenessLocal, 2),
WclosenessG = WClosenessGlobal
)
WBetweennessLocal <- betweenness(graph.net, weights=edgelist[,3])
WBetweennessGlobal <- mean(WBetweennessLocal)
netObj@betweenness <- list(
WbetweennessL = round(WBetweennessLocal, 2),
WbetweennessG = WBetweennessGlobal
)
WClusteringCoefLocal <- transitivity(graph.net, type="local",
weights=edgelist[,3])
WClusteringCoefGlobal <- transitivity(graph.net, type="global",
weights=edgelist[,3])
netObj@transitivity <- list(
WtransitivityL = round(WClusteringCoefLocal, 2),
WtransitivityG = WClusteringCoefGlobal
)
netObj
}
```

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