Removes reactions with no gene annotations

This function removes reaction vertices with no gene annotations as indicated by the parameter gene.attr, and connect their neighbour vertices to preserve graph connectivity. This is particularly meaningful when reactions are translocation or spontaneous reactions, which are not catalysed by genes.

simplifyReactionNetwork(
  reaction.graph,
  gene.attr = "genes",
  remove.missing.genes = TRUE,
  reconnect.threshold = vcount(reaction.graph)
)

Arguments

reaction.graph

A reaction network.

gene.attr

The attribute to be considered as "genes". Reactions missing this annotation, will be removed.

remove.missing.genes

If FALSE, only tranlocation and spontaneous reactions are removed, otherwise all rections with no gene annotations are removed.

reconnect.threshold

An argument passed to vertexDeleteReconnect

Value

A simplified reaction network.

See also

Other Network processing methods: expandComplexes(), makeMetaboliteNetwork(), makeReactionNetwork(), reindexNetwork(), rmSmallCompounds(), vertexDeleteReconnect()

Author

Ahmed Mohamed

Examples

 data(ex_sbml)
 rgraph <- makeReactionNetwork(ex_sbml, simplify=FALSE)
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...

 ## Removes all reaction nodes with no annotated genes.
 rgraph <- simplifyReactionNetwork(rgraph, remove.missing.genes=TRUE)