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")
)

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.

See also

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

Author

Ahmed Mohamed

Examples

    data(ex_sbml)

    sbml.removed <- rmSmallCompounds(ex_sbml, method="remove")
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...