man for exportSBML in the first version

man/exportSBML.Rd

+\name{exportSBML}
+\alias{exportSBML}
+
+\encoding{utf8}
+
+\title{Exports a Metabolic Network in SBML Format}
+
+\description{
+  The function exports a metabolic network from S4 object of the class \code{\link{modelorg}} in SBML format. The function
+  returns a success message if exported to SBML file is successfully built.
+}
+
+\usage{
+  exportSBML(morg=NULL,level=2,version=4,FbcLevel=0,
+             filename="export.xml",
+             recoverExtMet=TRUE,
+             printNotes=TRUE,
+             printAnnos=TRUE,
+             validation=FALSE)
+
+}
+
+\arguments{
+  \item{morg}{
+    An S4 object of the class \code{\link[sybil]{modelorg}}.
+  }
+  \item{level}{
+    A single integer value containing the SBML level for the exporting SBML file. \cr
+    Default: \code{2}.
+  }
+   \item{version}{
+    A single integer value containing the SBML version for the exporting SBML file. \cr
+    Default: \code{4}.
+  }
+  \item{FbcLevel}{
+    A single integer value containing the fbc package version for the exporting SBML file. \cr
+    Default: \code{2}.
+  }
+   \item{filename}{
+    SBML filename for exporting the model.
+    Default: \code{"export.xml"}.
+  }
+  \item{recoverExtMet}{
+    Boolean: recover external metabolites and refer them to compartment \code{"BOUNDARY"}.\cr 
+    Default: \code{TRUE}.
+  }
+  \item{printNotes}{
+    Boolean: print Notes from original SBML file .\cr
+    Default: \code{TRUE}.
+  }
+  \item{printAnnos}{
+    Boolean: print Annotations from original SBML file .\cr
+    Default: \code{TRUE}.
+  }
+  \item{validation}{
+    Boolean: print containing errors for xml file .\cr
+    Default: \code{TRUE}.
+  }
+
+}
+
+\details{
+  The library \code{libSBML} is used to export a \code{\link[sybil]{modelorg}}
+  to a SBML file.
+
+}
+
+\value{
+  A single character string for a success message.
+}
+
+\references{
+  The BiGG database \url{http://bigg.ucsd.edu/}.
+
+  Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+  LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+  880--881.
+
+  Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., (2010)
+  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic
+  reconstructions. \emph{BMC Bioinformatics} \bold{11}, 213.
+
+  Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø.  and
+  Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with
+  constraint-based models: the COBRA Toolbox. \emph{Nat Protoc} \bold{2},
+  727--738.
+
+  Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D.,
+  Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S.,
+  Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of
+  cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
+  \emph{Nat Protoc} \bold{6}, 1290--1307.
+}
+
+\author{
+  Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+  Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\note{
+  The function \code{exportSBML} makes use of the library
+  \code{libSBML} (\url{http://www.sbml.org}).
+}
+
+\seealso{
+  \code{\link{readSBMLmod}}
+}
+
+\examples{
+  dir  <- system.file(package = "sybilSBML", "extdata")
+  file <- file.path(dir, "ecoli_core_model.xml")
+  mod  <- readSBMLmod(file, bndCond = FALSE)
+  exportSBML(mod,level=3,version=1,FbcLevel=2)
+}
+
+\keyword{ IO }
+