rmSmallCompounds: Remove uniquitous compounds from a metabolic network

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

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")
    

ahmohamed/NetPathMiner documentation built on Oct. 31, 2024, 8:01 a.m.