Description Usage Arguments Value Author(s) See Also Examples
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.
1 | makeReactionNetwork(graph, simplify = FALSE)
|
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. |
A reaction network.
Ahmed Mohamed
Other Network processing methods: expandComplexes
,
makeMetaboliteNetwork
,
reindexNetwork
,
rmSmallCompounds
,
simplifyReactionNetwork
,
vertexDeleteReconnect
1 2 3 | ## Conver a metabolic network to a reaction network.
data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)
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