inst/AnnDbPkg-templates/MALARIA.DB/man/PATH.Rd
8cc745fe
 \name{@ANNOBJPREFIX@PATH}
 \alias{@ANNOBJPREFIX@PATH}
 \alias{@ANNOBJPREFIX@PATH2ORF}
 \title{Mappings between ORF identifiers and KEGG pathway identifiers}
 \description{
   KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
   for various organisms. @ANNOBJPREFIX@PATH maps ORF 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@
 
 }
 \references{
   \url{http://www.genome.ad.jp/kegg/}
 }
 \examples{
     x <- @ANNOBJPREFIX@PATH
     # Get the ORF 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@PATH2ORF)
     # Remove pathway identifiers that do not map to any ORF id
     xx <- xx[!is.na(xx)]
     if(length(xx) > 0){
         # The ORF identifiers for the first two elements of XX
         xx[1:2]
         # Get the first one
         xx[[1]]
     }
 }
 \keyword{datasets}