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runTest.ts

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    blockedReact.Rd 2.47 KiB
    \name{blockedReact}
    
    \alias{blockedReact}
    
    \title{
      Find Blocked Reactions in a Metabolic Network
    }
    
    \description{
      A blocked Reaction in a metabolic network can not be used by the network,
      given the stiochiometric matrix of the network and a set of input and output
      fluxes.
    }
    
    \usage{
      blockedReact(model,
                   tol = SYBIL_SETTINGS("TOLERANCE"),
                   exex = TRUE,
                   fld = FALSE,
                   retOptSol = FALSE,
                   verboseMode = 2,
                   ...)
    }
    
    \arguments{
      \item{model}{
        An object of class \code{\link{modelorg}}.
      }
      \item{tol}{
        Tolerance value.\cr
        Default: \code{SYBIL_SETTINGS("TOLERANCE")}.
      }
      \item{exex}{
        Boolean, if set to \code{TRUE}, exchange reactions found by
        \code{\link{findExchReact}} are excluded from the analysis.\cr
        Default: \code{TRUE}.
      }
      \item{fld}{
        Boolean.  Save the resulting flux distributions.\cr
        Default: \code{FALSE}
      }
      \item{retOptSol}{
        Boolean.  Return an object of class
        \code{\linkS4class{optsol_blockedReact}} or
        just a list containing the results.\cr
        Default: \code{FALSE}.
      }
      \item{verboseMode}{
        An integer value indicating the amount of output to stdout:
        0: nothing, 1: status messages, 2: like 1 plus a progress indicator.\cr
        Default: \code{2}.
      }
      \item{\dots}{
        Further arguments passed to \code{\linkS4class{sysBiolAlg}}.
        Argument \code{solverParm} is a good candidate.
      }
    }
    
    \details{
      A reaction \eqn{i} is considered to be \sQuote{blocked}, if its calculated
      reaction rate \eqn{v_i}{v[i]} is
      \eqn{-\mathrm{tol} < v_i < \mathrm{tol}}{-tol < v[i] < tol}.
      Reaction rates are calculated via linear optimization: maximizing and
      minimizing each reaction rate. If the difference of the maximum and the
      minimum is not larger than \code{tol}, that particular reaction is blocked,
      given the current side conditions (exchange fluxes).
    }
    
    \value{
      If argument \code{retOptsol} is set to \code{TRUE}, an object of class
      \code{\linkS4class{optsol_blockedReact}} is returned, otherwise a logical
      vector with length equal to the number of reactions of the network. If element
      \code{i} equals \code{TRUE}, reaction \code{i} is blocked.
    }
    
    \author{
      Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
    
      Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
    }
    
    
    \seealso{
      \code{\link{modelorg}},
      \code{\linkS4class{optsol_blockedReact}} and
      \code{\link{SYBIL_SETTINGS}}.
    }
    
    \keyword{optimize}