metabolites: Identify the list of metabolites for a set of stoichiometric...
In dosorio/minval: MINimal VALidation for Stoichiometric Reactions

metabolites

R Documentation

Identify the list of metabolites for a set of stoichiometric reactions

Description

This function identifies the list of metabolites for a set of stoichiometric reactions. If 'woCompartment' is 'TRUE' compartment label is removed. If 'uniques' is 'TRUE', list of uniques is returned.

Usage

metabolites(reactionList, woCompartment = FALSE, uniques = TRUE)

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] <=>

woCompartment

A boolean value 'TRUE' or 'FALSE' to indicate if compartment label should be removed

uniques

A boolean value 'TRUE' or 'FALSE' to indicate if uniques must be returned

Value

A list of metabolites for a set of stoichiometric reactions

Author(s)

Daniel Camilo Osorio <dcosorioh@tamu.edu>

Examples

# Extract metabolites of a stoichiometric reaction
metabolites(reactionList = "ADP[c] + Phosphoenolpyruvate[c] => ATP[c] + Pyruvate[c]")

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

# Extract unique metabolites
metabolites(reactionList = glycolysis$REACTION)

#' # Extract unique metabolites without compartments
metabolites(reactionList = glycolysis$REACTION, woCompartment = TRUE)

# Extract all metabolites
metabolites(reactionList = glycolysis$REACTION, uniques = FALSE)

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