Convert metabolic network to reaction network.

This function removes metabolite nodes keeping them as edge attributes. The resulting network contains reaction nodes only, where edges indicate that a metabolite produced by one reaction is consumed by the other.

makeReactionNetwork(graph, simplify = FALSE)

Arguments

graph

A metabolic network.

simplify

An option to remove translocation and spontaneous reactions that require no catalyzing genes. Translocation reactions are detected from reaction name (SBML, BioPAX), or by having identical substrates and products.

Value

A reaction network.

See also

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

Author

Ahmed Mohamed

Examples

  ## Conver a metabolic network to a reaction network.
 data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
 rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)
#> 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...