checkBalance: Evaluate the mass or charge balance for a set of...

In gibbslab/minval: MINimal VALidation for Stoichiometric Reactions

Evaluate the mass or charge balance for a set of stoichiometric reactions

Description

For a given set of stoichiometric reactions, this function evaluates the mass or charge balance using a reference data. The checkBalance function returns a boolean value 'TRUE' if the reaction is balanced. One of 'mFormula', 'mWeight' or 'mCharge' arguments must be given.

Usage

checkBalance(
  reactionList,
  referenceData,
  ids,
  mFormula = NULL,
  mWeight = NULL,
  mCharge = NULL,
  woCompartment = 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] <=>
referenceData	A chemical table containing data to evaluate the balance
ids	A mandatory ID of metabolite names column in the referenceData
mFormula	An optional ID of molecular formula column in the referenceData
mWeight	An optional ID of molecular weight column in the referenceData
mCharge	An optional ID of net charge column in the referenceData
woCompartment	A boolean value 'TRUE' or 'FALSE' to indicate if compartment label should be removed of stoichiometric reactions

Value

This function returns a boolean value 'TRUE' if reaction is balanced.

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')

# Loading extrernal chemical information
chemicalData <- read.csv2(system.file("extdata", "chemData.csv", package = "minval"))
head(chemicalData)

# Evaluating mass balance
checkBalance(
reactionList = glycolysis$REACTION,
referenceData = chemicalData,
ids = "NAME",
mFormula = "FORMULA"
)

gibbslab/minval documentation built on May 25, 2022, 5:20 a.m.