rmSmallCompounds

graph

How to handle small compounds. Either simply delete these vertices <code>"remove"</code> (default),
or make a separate vertex for each reaction they participate in <code>"duplicate"</code>.

method

small.comp.ls


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.


NetPathMiner is a general framework for network path
mining using genome-scale networks. It constructs networks from
KGML, SBML and BioPAX files, providing three network
representations, metabolic, reaction and gene representations.
NetPathMiner finds active paths and applies machine learning
methods to summarize found paths for easy interpretation. It
also provides static and interactive visualizations of networks
and paths to aid manual investigation.

Ahmed Mohamed

NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining
and Visualization

rmSmallCompounds function

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: Remove uniquitous compounds from a metabolic network

Description

Usage

Arguments

Value

See Also

Examples