characterizeReactions: Characterize stoichiometric reactions by compartments and...

In dosorio/minval: MINimal VALidation for Stoichiometric Reactions

Characterize stoichiometric reactions by compartments and reaction type

Description

For a given set of stoichiometric reactions, this function:

• Counts the number of reactions,

• Computes the relative frequency of each reaction type (transport, exchange and compartmentalized),

• Computes the relative frequency of reactions by compartment,

• Counts the number of unique metabolites,

• Computes the relative frequency of metabolites by compartment.

Usage

characterizeReactions(reactionList, rawOutput = FALSE)

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] <=>

rawOutput

A boolean value 'TRUE' or 'FALSE' if raw data should be returned instead of computed values.

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')

# Characterizing the reactions
characterizeReactions(reactionList = glycolysis$REACTION)

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