\Header{GEO-class}{Class "GEO" represents a GEO object that reads/downloads data
from the GEO web site}
\alias{GEO}{GEO-class}
\keyword{classes}{GEO-class}
\begin{Description}\relax
The GEO web site contains data files represented by GEO
accession numbers. Class GEO reads/downloads data files from the site
if correct url and GEO accession numbers are provided\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("UG", ...)}.
A constructor (GEO) is available and should be used to instatiate
objects of this class\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{srcUrl}:] Object of class \code{"character", from class
        "pubRepo"} - a character string for the url of a CGI script that
handles data requests, which is:
\url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?} at the time of
writing 
}\end{Section}
\begin{Section}{Extends}
Class \code{"pubRepo"}, directly.\end{Section}
\begin{Section}{Methods}
\describe{
\item[readData] \code{signature(object = "GEO")}: reads data from
GEO and then parses the data to a matrix
}\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
Programming with data\end{References}
\begin{SeeAlso}\relax
\code{\Link{queryGEO}},\code{\Link{pubRepo-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
    if(interactive()){
        geo <- GEO("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
        # The GEOAccNum may be invalid due to changes at GEO site
        data <- readData(geo, GEOAccNum = "GPL16" )
    }
\end{ExampleCode}
\end{Examples}

