diff --git a/man/exportSBML.Rd b/man/exportSBML.Rd new file mode 100644 index 0000000000000000000000000000000000000000..a50105ed89024a6da86102754a05de9437fdc3bf --- /dev/null +++ b/man/exportSBML.Rd @@ -0,0 +1,119 @@ +\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 } +