makeReactionNetwork: Convert metabolic network to reaction network.

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Convert metabolic network to reaction network.

Description

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.

Usage

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.

Author(s)

Ahmed Mohamed

See Also

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

Examples

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

ahmohamed/NetPathMiner documentation built on Oct. 31, 2024, 8:01 a.m.