\Header{KEGG-class}{Class "KEGG" a sub-class of pubRepo to get/process pathway and
enzyme information}
\alias{findIDNPath}{KEGG-class}
\alias{KEGG}{KEGG-class}
\alias{mapLL2ECNPName}{KEGG-class}
\keyword{classes}{KEGG-class}
\begin{Description}\relax
This class is a sub-class of pubRepo with source specific
functions to get/process data from KEGG
{\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}} to obtain pathway and
emzyme information for genes\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("KEGG", ...)}.
A constructor (KEGG) is available and should be used to instantiate
objects of this class\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{organism}:] Object of class \code{"character", from
        class "UG"} a character string for the organism of concern
\item[\code{srcUrl}:] Object of class \code{"character", from class
        "UG"} a character string for the url where source data are
stored (\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}) at the
time of coding
\item[\code{parser}:] Object of class \code{"character", from class
        "UG"} not in use
\item[\code{baseFile}:] Object of class \code{"character", from
        class "UG"} not in use
}\end{Section}
\begin{Section}{Extends}
Class \code{"UG"}, directly.
Class \code{"pubRepo"}, by class "UG".\end{Section}
\begin{Section}{Methods}
\describe{
\item[findIDNPath] \code{signature(object = "KEGG")}: Finds the
mappings between KEGG ids and pathway names
\item[mapLL2ECNPName] \code{signature(object = "KEGG")}: Maps
LocusLink ids to enzyme ids and pathway names
}\end{Section}
\begin{Note}\relax
This class is part of the Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through R\end{Note}
\begin{Author}\relax
Jianhua Zhang\end{Author}
\begin{References}\relax
\url{www.genome.ad.jp/kegg/}\end{References}
\begin{SeeAlso}\relax
\code{\Link{pubRepo-class}}, \code{\Link{UG-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# The url (\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}) may change but
# was correct at the time of coding
url <-  getSrcUrl("KEGG")
kegg <- KEGG(srcUrl = url, organism = "human")
## This part takes a while to finish (due to a large number of files to
## process) and is thus commented out. Try it only if you are really
## patient
# pathNEnzyme <- mapLL2ECNPName(kegg)
\end{ExampleCode}
\end{Examples}

