bio3d (version 2.3-4)

network.amendment: Amendment of a CNA Network According To A Input Community Membership Vector.

Description

This function changes the ‘communities’ attribute of a ‘cna’ class object to match a given membership vector.

Usage

network.amendment(x, membership, minus.log=TRUE)

Arguments

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.

Value

Returns a ‘cna’ class object with the attributes changed according to the membership vector provided.

Details

This function is useful, in combination with ‘community.tree’, for inspecting different community partitioning options of a input ‘cna’ object. See examples.

See Also

cna, community.tree, summary.cna

Examples

# NOT RUN {
# 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)

}
# }