vertexDeleteReconnect {NetPathMiner} | R Documentation

## Network editing: removing vertices and connecting their neighbours

### Description

This function removes vertices given as `vids` and connects their neighbours as long as the shortest path beween the neighbours are below the `reconnect.threshold`.

### Usage

    vertexDeleteReconnect(graph, vids, reconnect.threshold = vcount(graph),
      copy.attr = NULL)

### Arguments

`graph` | A reaction network.
`vids` | Vertex ids to be removed.
`reconnect.threshold` | If the shortest path between vertices is larger than this threshold, they are not reconnected.
`copy.attr` | A function, or a list of functions, combine edge attributes. Edge attributes of new edges (between reconnected neighbours) are obtained by combining original edges attributes along the shortest path between reconnected neighbors.

### Value

A modified graph.

### Author(s)

Ahmed Mohamed

### See Also

Other Network processing methods: `expandComplexes`, `makeMetaboliteNetwork`, `makeReactionNetwork`, `reindexNetwork`, `rmSmallCompounds`, `simplifyReactionNetwork`

### Examples

     ## Remove all reaction vertices from a bipartite metabolic network
    	##  keeping only metabolite vertices.
     data(ex_sbml)
     graph <- vertexDeleteReconnect(ex_sbml, vids=which(V(ex_sbml)$reactions))

[Package NetPathMiner version 1.20.0 Index]