R: Prune A cna Network Object

prune.cna {bio3d} | R Documentation

## 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.

### 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.

### Value

A cna class object, see function `cna` for details.

### Note

Some improvements to this function are required, including a better effort to preserve the original community structure rather than calculating a new one. Also may consider removing nodes form the raw.network object that is returned also.

### Author(s)

Barry Grant

### References

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

### See Also

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

### Examples

    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)

    }

[Package bio3d version 2.4-2 Index]