makeReactionNetwork: Convert metabolic network to reaction network.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/netProcess.R

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

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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

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

NetPathMiner documentation built on Nov. 8, 2020, 8:20 p.m.