vertexDeleteReconnect | R Documentation |
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
.
vertexDeleteReconnect(graph, vids, reconnect.threshold = vcount(graph),
copy.attr = NULL)
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. |
A modified graph.
Ahmed Mohamed
Other Network processing methods: expandComplexes
,
makeMetaboliteNetwork
,
makeReactionNetwork
,
reindexNetwork
,
rmSmallCompounds
,
simplifyReactionNetwork
## 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))
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