Amendment of a CNA Network According To A Input Community Membership Vector.
This function changes the ‘communities’ attribute of a ‘cna’ class object to match a given membership vector.
network.amendment(x, membership, minus.log=TRUE)
x |
A protein network graph object as obtained from the ‘cna’ function. |
membership |
A numeric vector containing the new community membership. |
minus.log |
Logical. Whether to use the minus.log on the cij values. |
This function is useful, in combination with ‘community.tree’, for inspecting different community partitioning options of a input ‘cna’ object. See examples.
Returns a ‘cna’ class object with the attributes changed according to the membership vector provided.
Guido Scarabelli
# PDB server connection required - testing excluded
if (!requireNamespace("igraph", quietly = TRUE)) {
message('Need igraph installed to run this example')
} else {
##-- Build a CNA object
pdb <- read.pdb("4Q21")
modes <- nma(pdb)
cij <- dccm(modes)
net <- cna(cij, cutoff.cij=0.2)
##-- Community membership vector for each clustering step
tree <- community.tree(net, rescale=TRUE)
## Produce a new k=7 membership vector and CNA network
memb.k7 <- tree$tree[ tree$num.of.comms == 7, ]
net.7 <- network.amendment(net, memb.k7)
plot(net.7, pdb)
print(net)
print(net.7)
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.