Find and fill gaps in a metabolic network

Description

This function identifies the gaps and fills it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function.

Usage

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gapFill(reactionList, reference, limit = 0.25, woCompartment = FALSE,
  consensus = FALSE)

Arguments

reactionList

A set of 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 reactionList

limit

An addition cost value to be used as a limit to select reactions to be added. Is calculated as NumberNewMetabolites/NumerOfMetabolites for each reaction.

woCompartment

A boolean value TRUE to define if compartment labels should be removed of the reactionList stoichiometric reactions, FALSE is used as default.

consensus

A boolean value TRUE to define if reactionList and newReactions should be reported as a unique vector or FALSE if just newReactions should be reported.

Author(s)

Kelly Botero <kjboteroo@unal.edu.co> - Maintainer: Daniel Camilo Osorio <dcosorioh@unal.edu.co>

See Also

additionCost function documentation.

Examples

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## Not run: 
# Downloading stoichiometric reactions
all <- getReference(organism = "all",sep = ";")
eco <- getReference(organism = "eco",sep = ";")

# Filtering reactions
all <- mapReactions(reactionList = all$reaction%in%eco$reaction,
                    referenceData = all,
                    by = "bool",
                    inverse = TRUE)
                    
# gapFill
gapFill(reactionList = eco$reaction,
        reference = all$reaction, 
        limit = 0.25,
        woCompartment = TRUE,
        consensus = FALSE)
## End(Not run)