Remove uniquitous compounds from a metabolic network

Share:

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

1
2
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

1
2
3
4
5
    data(ex_sbml)
        
    
    sbml.removed <- rmSmallCompounds(ex_sbml, method="remove")
    

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.