gapFill: Find and fill gaps in a metabolic network
In gibbslab/g2f: Find and Fill Gaps in Metabolic Networks

Description Usage Arguments Author(s) See Also Examples

View source: R/gapFill.R

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

gapFill(
  reactionList,
  reference,
  limit = 0.25,
  nRun = 5,
  woCompartment = FALSE,
  consensus = FALSE
)

`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.
`nRun`	The number of iterations to search for new gaps and fill them according to the score, the default is five.
`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.

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

additionCost function documentation.

## 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)