stoichiometricMatrix: Build the stoichiometric matrix for a set of stoichiometric...

In dosorio/minval: MINimal VALidation for Stoichiometric Reactions

Build the stoichiometric matrix for a set of stoichiometric reactions

Description

A set of stoichiometric reactions is often represented in a more compact form called the stoichiometry matrix. If a metabolic network has n reactions and m participating metabolites, then the stoichiometry matrix will have correspondingly m rows and n columns. Values in the stoichiometric matrix represent the metabolites coefficients in each reaction.

Usage

stoichiometricMatrix(reactionList)

Arguments

reactionList

A set of stoichiometric reaction with the following characteristics: Arrows symbols must be given in the form '=>' or '<=>' Inverse arrow symbols '<=' or other types as: '-->', '<==>', '->' will not be parsed and will lead to errors. Arrow symbols and plus signs (+) must be surrounded by a space character Stoichiometric coefficients must be surrounded by a space character and not by parentheses. Each metabolite must have only one stoichiometric coefficient, substituents must be joined to metabolite name by a hyphen (-) symbol. Exchange reactions have only one metabolite before arrow symbol Compartments must be given between square brackets ([compartment]) joined at the end of metabolite name Some examples of valid stoichiometric reactions are: H2O[c] + Urea-1-Carboxylate[c] <=> 2 CO2[c] + 2 NH3[c] ADP[c] + Phosphoenolpyruvate[c] => ATP[c] + Pyruvate[c] CO2[c] <=>

Value

The stoichiometric matrix for a given set of stoichiometric reactions

Author(s)

Daniel Camilo Osorio <[e-mail]>

Examples

# Loading a set of stoichiometric reactions
glycolysis <- read.csv(system.file("extdata/glycolysisModel.csv",package = "minval"), sep='\t')

# Building the stoichiometric matrix
stoichiometricMatrix(reactionList = glycolysis$REACTION)

dosorio/minval documentation built on May 24, 2022, 7:42 p.m.