rmSmallCompounds: Remove uniquitous compounds from a metabolic network

Description Usage Arguments Value Author(s) See Also Examples

View source: R/netProcess.R

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

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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, makeReactionNetwork, simplifyReactionNetwork, vertexDeleteReconnect

Examples

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

NetPathMiner documentation built on May 31, 2017, 1:28 p.m.