\HeaderA{agPATH}{Mappings between probe identifiers and KEGG pathway identifiers}{agPATH}
\keyword{datasets}{agPATH}
\begin{Description}\relax
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
for various organisms. agPATH maps probe identifiers to the
identifiers used by KEGG for pathways in which the genes represented
by the probe identifiers are involved
\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:

Tair: \url{ftp://ftp.arabidopsis.org/home/tair//ath/ath_gene_map.tab}
Built: N/A

Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt}
Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes}
Tair: \url{ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.08012006.txt}
Built: N/A

Package built Wed Sep  6 11:22:37 2006
\end{Details}
\begin{References}\relax
\url{http://www.genome.ad.jp/kegg/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert the environment to a list
    xx <- as.list(agPATH)
    # Remove probe identifiers that do not map to any pathway id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The pathway identifiers for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 
\end{ExampleCode}
\end{Examples}

