g2f (version 0.2)

additionCost: Calculate the cost of addition of a stoichiometric reaction in a metabolic network

Description

For a given set of stoichiometric reactions this function calculates the cost of addition in a reference metabolic network. The cost is calculated by dividing the amount of non included metabolites in the reference metabolic network over the total number of metabolites involved in the reaction.

Usage

additionCost(reaction, reference)

Arguments

reaction

A stoichiometric reaction with the following format:

"H2O[c] + Urea-1-carboxylate[c] <=> 2 CO2[c] + 2 NH3[c]"

Where arrows and plus signs are surrounded by a "space character". It is also expected that stoichiometry coefficients are surrounded by spaces, (nothe the "2" before the CO2[c] or the NH3[c]). It also expects arrows to be in the form "=>" or "<=>". Meaning that arrows like "==>", "<==>", "-->" or "->" will not be parsed and will lead to errors.

reference

A set of stoichiometric reaction with the same format of reaction.

Examples

# NOT RUN {
# Downloading stoichiometric reactions of reference
hsa <- getReference(organism = "hsa")

# Calculating cost
additionCost(reaction = "alpha-Amino acid + H2O + NAD+ <=> 2-Oxo acid + Ammonia + NADH + H+",
             reference = hsa$reaction)
# }