\HeaderA{org.Sc.sgdPATH}{Mappings between ORF identifiers and KEGG pathway identifiers}{org.Sc.sgdPATH}
\aliasA{org.Sc.sgdPATH2ORF}{org.Sc.sgdPATH}{org.Sc.sgdPATH2ORF}
\keyword{datasets}{org.Sc.sgdPATH}
\begin{Description}\relax
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
for various organisms. org.Sc.sgdPATH maps ORF identifiers to the
identifiers used by KEGG for pathways.  The reverse map
org.Sc.sgdPATH2ORF maps back from KEGG pathway IDs to the ORF
identifiers.
\end{Description}
\begin{Details}\relax
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: KEGG GENOME ( ftp://ftp.genome.jp/pub/kegg/genomes ) on 2008-Sep2
\end{Details}
\begin{References}\relax
\url{http://www.genome.ad.jp/kegg/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    x <- org.Sc.sgdPATH
    # 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]]
    }
    # Convert the object to a list
    xx <- as.list(org.Sc.sgdPATH2ORF)
    # 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]]
    }
\end{ExampleCode}
\end{Examples}

