gapFill.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/gapFill.R
\name{gapFill}
\alias{gapFill}
\title{Find and fill gaps in a metabolic network}
\usage{
gapFill(
  reactionList,
  reference,
  limit = 0.25,
  nRun = 5,
  woCompartment = FALSE,
  consensus = FALSE
)
}
\arguments{
\item{reactionList}{A set of stoichiometric reaction with the following format:

\code{"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 "\code{=>}" or "\code{<=>}".
Meaning that arrows like "\code{==>}", "\code{<==>}", "\code{-->}" or "\code{->}" will not be parsed and will lead to errors.}

\item{reference}{A set of stoichiometric reaction with the same format of reactionList}

\item{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.}

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

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

\item{consensus}{A boolean value \code{TRUE} to define if reactionList and newReactions should be reported as a unique vector or \code{FALSE} if just newReactions should be reported.}
}
\description{
This function identifies the gaps and fills it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function.
}
\examples{
\dontrun{
# 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
)
}
}
\seealso{
\code{additionCost} function documentation.
}
\author{
Kelly Botero <kjboteroo@unal.edu.co> - Maintainer: Daniel Camilo Osorio <dcosorioh@unal.edu.co>
}