Remove uniquitous compounds from a metabolic network
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.
rmSmallCompounds(graph, method = c("remove", "duplicate"), small.comp.ls = NPMdefaults("small.comp.ls"))
A metabolic network.
How to handle small compounds. Either simply delete these vertices
A list of small compounds to be used.
A modified graph, with the small compounds removed or duplicated.
Other Network processing methods:
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data(ex_sbml) sbml.removed <- rmSmallCompounds(ex_sbml, method="remove")