inst/AnnDbPkg-templates/NCBIORG.DB/man/PATH.Rd
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 \name{@ANNOBJPREFIX@PATH}
 \alias{@ANNOBJPREFIX@PATH}
 \alias{@ANNOBJPREFIX@PATH2EG}
 \title{Mappings between Entrez Gene identifiers and KEGG pathway identifiers}
 \description{
   KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
   for various organisms. @ANNOBJPREFIX@PATH maps entrez gene identifiers to the
   identifiers used by KEGG for pathways
 }
 \details{
   Each KEGG pathway has a name and identifier. Pathway name for a given pathway
   identifier can be obtained using the KEGG data package that can either be
   built using AnnBuilder or downloaded from Bioconductor
   \url{http://www.bioconductor.org}.
 
   Graphic presentations of pathways are searchable at
   url http://www.genome.ad.jp/kegg/pathway.html by using pathway identifiers as
   keys.   
 
   Mappings were based on data provided by: @PATHSOURCE@
 
 }
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 \references{
   \url{http://www.genome.ad.jp/kegg/}
 }
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 \seealso{
   \itemize{
     \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
           the \code{select()} interface.
   }
 }
 
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 \examples{
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 ## select() interface:
 ## Objects in this package can be accessed using the select() interface
 ## from the AnnotationDbi package. See ?select for details.
 
 ## Bimap interface:
 x <- @ANNOBJPREFIX@PATH
 # Get the entrez gene identifiers that are mapped to a KEGG pathway ID
 mapped_genes <- mappedkeys(x)
 # Convert to a list
 xx <- as.list(x[mapped_genes])
 if(length(xx) > 0) {
   # Get the PATH for the first five genes
   xx[1:5]
   # Get the first one
   xx[[1]]
 }
 
 # For the reverse map:
 # Convert the object to a list
 xx <- as.list(@ANNOBJPREFIX@PATH2EG)
 # Remove pathway identifiers that do not map to any entrez gene id
 xx <- xx[!is.na(xx)]
 if(length(xx) > 0){
     # The entrez gene identifiers for the first two elements of XX
     xx[1:2]
     # Get the first one
     xx[[1]]
 }
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 }
 \keyword{datasets}