\Header{GO-class}{Class "GO" a class to handle data from Gene Ontology}
\alias{GO}{GO-class}
\keyword{classes}{GO-class}
\begin{Description}\relax
This class is sub-class of pubRepo that is implemented
specifically to parse data from Gene Ontology. \code{\Link{readData}}
has been over wirtten to process Gene Ontology data\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("GO", ...)}.
A constructor (\code{\Link{GO}} is available and should be used to
instatiate objects of GO\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{srcUrl}:] Object of class \code{"character", from class
        "pubRepo"} a character string for the url of the source data
from Gene Ontology
\item[\code{parser}:] Object of class \code{"character", from class
        "pubRepo"} not in use
\item[\code{baseFile}:] Object of class \code{"character", from
        class "pubRepo"} not in use
}\end{Section}
\begin{Section}{Extends}
Class \code{"pubRepo"}, directly.\end{Section}
\begin{Section}{Methods}
\describe{
\item[readData] \code{signature(object = "GO")}: Downloads/processes
go\_xxx-termdb from Gene Ontology, where xxx is date. If argument
xml is set to be TRUE, the data file will be parsed and a matrix
with three columns will be returned. The first column is for GO
ids, second for the GO ids of its direct parents, and third for
the ontology term defined by Gene Ontology. Otherwise, the data
(not in xml form) will be read in using \code{\Link{readLines}}
}\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{http://www.godatabase.org}\end{References}
\begin{SeeAlso}\relax
\code{\Link{pubRepo-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Read a truncated version of GO.xml from Bioconductor
go <- GO(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml")
goxml <- readData(go, xml = TRUE)
\end{ExampleCode}
\end{Examples}

