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 %  ./getKEGGPathways.R
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 \name{getKEGGPathways}
 \alias{getKEGGPathways}
 
 
 \title{Builds a graph for each of the KEGG pathways}
 
 \description{
  Builds a graph for each of the KEGG pathways.
 }
 
 \usage{getKEGGPathways(path=NULL, rootPath="networkData/ftp.genome.jp/pub/kegg/xml/kgml", organism="hsa", metaTag=c("non-metabolic", "metabolic"), pattern=NULL, verbose=FALSE)}
 
 \arguments{
   \item{path}{A \code{\link[base]{character}} value, the local _full_ path of KGML data.}
   \item{rootPath}{A \code{\link[base]{character}} value, the local _root_ path of KGML data.}
   \item{organism}{A \code{\link[base]{character}} value specifying the organism whose
      pathways should be considered. Defaults to "hsa" (Homo Sapiens).}
   \item{metaTag}{A \code{\link[base]{character}} value, specifying the type of pathways to
     be considered ("metabolic" or "non-metabolic"). Defaults to "non-metabolic".}
   \item{pattern}{An optional \code{\link[base]{character}} value specifying a file name pattern to
     look for.}
   \item{verbose}{If \code{\link[base:logical]{TRUE}}, extra information is output.}
 }
 
 \value{
   A \code{\link[base]{list}} containing a \code{\link[=graph-class]{graph}} object for each KEGG pathway with at least one edge.
 }
 
 \details{If 'path' is supplied, KGML files in this directory are loaded.
   Otherwise, KGML files are assumed to be in
   <rootPath>/<metaTag>/"organisms"/<organism>, which mirrors the
  structure of the KEGG KGML file repository.
 }
 
 \author{Laurent Jacob, Pierre Neuvial and Sandrine Dudoit}
 
 \seealso{
   \code{\link{parseKGML}}
   \code{\link{KEGGpathway2Graph}}
 }
 
 \examples{

 library("Rgraphviz")

 library("KEGGgraph")
 
 ## example of KGML files
 path <- system.file("extdata", package="KEGGgraph")
 grList <- getKEGGPathways(path=path, verbose=TRUE)
 print(grList)
 
 graph <- grList[[1]]
 plotKEGGgraph(graph)
 
 \dontrun{
   ## Download all human KGML pathways locally
   pathname <- system.file("downloadScripts", "downloadKeggXmlFiles.R", package="DEGraph")
   source(pathname)
 
   ## Load some of them
   grList <- getKEGGPathways(pattern="040", verbose=TRUE)
   print(grList)
 
   graph <- grList[[1]]
   plotKEGGgraph(graph)
 }
 }