Skip to content
Snippets Groups Projects
Select Git revision
  • 52b45dc577e20a76527ec8348530c6c1077e41d5
  • master default protected
  • dev
  • sybilNLO
  • gprBug
  • maximumtotalflux
  • easyConstraint
  • switchbug
  • thuong
  • momafix
  • rmReactBug
11 results

oneFluxDel.Rd

  • Code owners
    Assign users and groups as approvers for specific file changes. Learn more.
    oneFluxDel.Rd 2.45 KiB
    \name{oneFluxDel}
    \alias{oneFluxDel}
    
    \encoding{utf8}
    
    \title{Single Flux Deletion Experiment}
    
    \description{
      Single reaction (flux) deletion analysis.
    }
    
    \usage{
      oneFluxDel(model, react = c(1:react_num(model)),
                 lb = rep(0, length(react)),
                 ub = rep(0, length(react)),
                 checkOptSolObj = FALSE, ...)
    }
    
    \arguments{
      \item{model}{
        An object of class \code{\linkS4class{modelorg}}.
      }
      \item{react}{
        An object of class \code{\linkS4class{reactId}} or character or integer
        containing reaction id's to constrain to zero one by one.\cr
        Default: all reactions present in argument \code{model}.
      }
      \item{lb}{
        A numeric vector of the same length as \code{react} containing the lower
        bounds for the reaction rates of reactions (variables) given in argument
        \code{react}.\cr
        Default: \code{0} for all reactions in \code{react}, zero flux through all
        reactions.
      }
      \item{ub}{
        A numeric vector of the same length as \code{react} containing the lower
        bounds for the reaction rates of reactions (variables) given in argument
        \code{react}.\cr
        Default: \code{0} for all reactions in \code{react}, zero flux through all
        reactions.
      }
      \item{checkOptSolObj}{
        A single logical value. If set to \code{TRUE}, a warning will be generated,
        if not all optimizations ended successful.\cr
        Default: \code{FALSE}.
      }
      \item{\dots}{
        Further arguments passed to \code{\link{optimizer}}.  Important ones are
        \code{algorithm} in order to set the algorithm to use or \code{solverParm}
        in order to set parameter values for the optimization software.
      }
    }
    
    \details{
      The function \code{oneFluxDel} studies the effect of constraining single
      fluxes to zero flux rates on the phenotype of the metabolic network. The
      function performs \eqn{n} optimizations with \eqn{n} being the number of
      reaction id's given in argument \code{react}. Each optimization corresponds
      to the removal of one reaction.
    }
    
    \value{
      An object of class \code{\linkS4class{optsol_fluxdel}}.
    }
    
    \author{
      Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
    
      Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
    }
    
    
    \seealso{
      \code{\link{modelorg}}, \code{\linkS4class{optsol}},
      \code{\linkS4class{optsol_fluxdel}},
      \code{\link{checkOptSol}}, \code{\link{optimizer}} and
      \code{\link{SYBIL_SETTINGS}}.
    }
    
    \examples{
      data(Ec_core)
      Ec_ofd <- oneFluxDel(Ec_core)
    }
    
    \keyword{optimize}