gapFind: Find gaps in a metabolic network

Description Usage Arguments Author(s)

View source: R/gapFind.R

Description

This function identifies the gaps (metabolites not produced or not consumed in any other reaction or just involved in one reaction) for a set of stoichometric reactions

Usage

1
gapFind(reactionList, removeExchange = FALSE)

Arguments

reactionList

A set of stoichiometric reaction with the following format:

"H2O[c] + Urea-1-carboxylate[c] <=> 2 CO2[c] + 2 NH3[c]"

Where arrows and plus signs are surrounded by a "space character". It is also expected that stoichiometry coefficients are surrounded by spaces, (nothe the "2" before the CO2[c] or the NH3[c]). It also expects arrows to be in the form "=>" or "<=>". Meaning that arrows like "==>", "<==>", "-->" or "->" will not be parsed and will lead to errors.

removeExchange

A boolean value FALSE to ignore the exchange reactions to identify the gaps.

Author(s)

Daniel Osorio <dcosorioh@unal.edu.co>


kellybotero/G2F documentation built on Dec. 5, 2020, 12:34 p.m.