bio3d (version 2.3-4)

prune.cna: Prune A cna Network Object

Description

Remove nodes and their associated edges from a cna network graph.

Usage

prune.cna(x, edges.min = 1, size.min = 1)

Arguments

x

A protein network graph object as obtained from the ‘cna’ function.

edges.min

A single element numeric vector specifying the minimum number of edges that retained nodes should have. Nodes with less than ‘edges.min’ will be pruned.

size.min

A single element numeric vector specifying the minimum node size that retained nodes should have. Nodes with less composite residues than ‘size.min’ will be pruned.

Value

A cna class object, see function cna for details.

Details

This function is useful for cleaning up cna network plots by removing, for example, small isolated nodes. The output is a new cna object minus the pruned nodes and their associated edges. Node naming is preserved.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

cna, summary.cna, vmd.cna, plot.cna

Examples

# NOT RUN {
if (!requireNamespace("igraph", quietly = TRUE)) {
   message('Need igraph installed to run this example')
} else {

# Load the correlation network
attach(hivp)

# Read the starting PDB file to determine atom correspondence
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)

# Plot coarse grain network based on dynamically coupled communities
par(mfcol=c(1,2), mar=c(0,0,0,0))
plot.cna(net)

# Prune network
dnet <- prune.cna(net, edges.min = 1)
plot(dnet)

detach(hivp)

}
# }