rmSmallCompounds {NetPathMiner} | R Documentation

## Remove uniquitous compounds from a metabolic network

### Description

This function removes uniquitous compounds (metabolites connected to numerous reactions) from a metabolic network.These compounds are reaction cofactors and currency compounds, such as ATP, CO2, etc. A path through these metabolites may not be bioloigcally meaningful. The defualt small compound list is derived from Reactome, containing keeg.compound, pubchem.compound, ChEBI and CAS identifiers.

### Usage

    rmSmallCompounds(graph, method = c("remove", "duplicate"),
      small.comp.ls = NPMdefaults("small.comp.ls"))

### Arguments

`graph` | A metabolic network.
`method` | How to handle small compounds. Either simply delete these vertices `"remove"` (default), or make a separate vertex for each reaction they participate in `"duplicate"`.
`small.comp.ls` | A list of small compounds to be used.

### Value

A modified graph, with the small compounds removed or duplicated.

### Author(s)

Ahmed Mohamed

### See Also

Other Network processing methods: `expandComplexes`, `makeMetaboliteNetwork`, `makeReactionNetwork`, `reindexNetwork`, `simplifyReactionNetwork`, `vertexDeleteReconnect`

### Examples

        data(ex_sbml)

        sbml.removed <- rmSmallCompounds(ex_sbml, method="remove")

[Package NetPathMiner version 1.20.0 Index]