Description Usage Arguments Author(s) Examples
This function calculates the addition-cost of a stoichiometric reaction in a metabolic network. The cost is computed for each reaction as the ratio of metabolites not included in the reference metabolic network over the total number of metabolites involved in the reaction.
1 | additionCost(reactionList, reference)
|
reactionList |
A set of stoichiometric reaction with the following characteristics:
Some examples of valid stoichiometric reactions are:
|
reference |
A different set of stoichiometric reactions with the same format of reactionList. This is the metabolic network expected to gap filling. |
Daniel Camilo Osorio <dcosorioh@unal.edu.co>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | # Generate a reference, a vector of stoichiometric reactions as described above.
example_reference <- vector()
example_reference[1] <- "A + B => C + D"
example_reference[2] <- "B + D => E"
# Generate a set of reactions to compute the addition cost.
example_reactionList <- vector()
example_reactionList[1] <- "A + E => F + G"
example_reactionList[2] <- "A + E <=> F"
# The addition cost function will identify those metabolites not included in
# the reference (F and G) and will compute the addition cost for each reaction
# as the ratio of the number of metabolites not included in the reference
# over the total of metabolites in the reaction (2/4 and 1/3 respectively).
additionCost(reactionList = example_reactionList, reference = example_reference)
# [1] 0.5000000 0.3333333
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