makeReactionNetwork {NetPathMiner} | R Documentation

## 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)

[Package NetPathMiner version 1.28.0 Index]