geneDeletion.Rd

\name{geneDeletion}
\alias{geneDeletion}

\encoding{utf8}

\title{
  Gene Deletion Experiments
}

\description{
  The function \code{geneDeletion} studies the effect of \eqn{n} in silico gene
  deletions on the phenotype of a metabolic network. The value of \eqn{n} is the
  number of genes knocked-out simultaneously.
}

\usage{
  geneDeletion(model, genes, combinations = 1,
               lb = NULL, ub = NULL, checkOptSolObj = FALSE, ...)
}

\arguments{
  \item{model}{
    An object of class \code{\linkS4class{modelorg}}.
  }
  \item{genes}{
    Character or Integer: the genes to delete (see Details below).
  }
  \item{combinations}{
    A single integer value. If \code{combinations > 1} and \code{genes} is not a
    matrix, \code{combinations} is the number of elements from \code{genes}
    taken at a time while building all combinations of the elements in
    \code{genes} (see Details below).\cr
    Default: \code{1}.
  }
  \item{lb}{
    A numeric vector containing the lower bounds for the reaction rates of
    reactions (variables) affected by the genes given in argument
    \code{genes}. If set to \code{NULL}, all reactions affected will be
    constrained to zero.\cr
    Default: \code{NULL}.
  }
  \item{ub}{
    A numeric vector containing the upper bounds for the reaction rates of
    reactions (variables) affected by the genes given in argument
    \code{genes}. If set to \code{NULL}, all reactions affected will be
    constrained to zero.\cr
    Default: \code{NULL}.
  }
  \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{
  If argument \code{genes} is a matrix of character values (gene id's) or
  integers (pointers to gene id's), each column is treated as one deletion
  experiment. If the matrix is made up of integers, a zero entry means no gene.
  
  If argument \code{genes} is a character vector or integer, the argument
  \code{combinations} gives the number of gene id's taken each time in order
  to build all possible combinations of \code{genes}. A matrix is constructed
  using \code{\link{combn}}. The value of argument \code{combinations} gives the
  number of genes, which are knocked-out simultaneously. The default value