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

In dosorio/minval: MINimal VALidation for Stoichiometric Reactions

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

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")

# 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)

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