minval (version 0.8-2)

orphanMetabolites: Identify the orphan metabolites of a set of stoichiometric reactions

Description

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

Usage

orphanMetabolites(reactionList, actingAs = NULL, byCompartment = FALSE)
orphanReactants(reactionList, byCompartment = FALSE)
orphanProducts(reactionList, byCompartment = 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] <=>

actingAs

A text string that specifies the type of metabolite to be returned; only 'reactant' and 'product' are supported.

byCompartment

A boolean value 'TRUE' or 'FALSE' to indicate if orphan reactants should be reported by compartment

Value

If byCompartment == FALSE, a vector with orphan reactants is returned, in opposite case a list is returned. If actingAs == 'reactant', metabolites not produced in any other reaction or just are involved in one reaction are returned. If actingAs == 'products', metabolites not consumed in any other reaction or just are involved in one reaction are returned.

Functions

• orphanReactants: Identify the orphan reactants of a set of stoichometric reactions

• orphanProducts: Identify the orphan products of a set of stoichometric reactions

Examples

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

# Identify orphan metabolites
orphanMetabolites(reactionList = glycolysis$REACTION)

# Identify orphan reactants
orphanReactants(reactionList = glycolysis$REACTION)

# Identify orphan products
orphanProducts(reactionList = glycolysis$REACTION)

# Identify orphan metabolites by compartment
orphanMetabolites(reactionList = glycolysis$REACTION, byCompartment = TRUE)
# }