\HeaderA{getGEOfile}{Download a file from GEO soft file to the local machine}{getGEOfile}
\keyword{IO}{getGEOfile}
\begin{Description}\relax
This function simply downloads a SOFT format file associated with the
GEO accession number given.
\end{Description}
\begin{Usage}
\begin{verbatim}
getGEOfile(GEO, destdir = tempdir(), amount = c("full", "brief", "quick", "data"))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{GEO}] Character string, the GEO accession for download (eg.,
GDS84, GPL96, GSE2553, or GSM10)
\item[\code{destdir}] Directory in which to store the resulting downloaded
file.  Defaults to tempdir()
\item[\code{amount}] Amount of information to pull from GEO.  Only applies to
GSE, GPL, or GSM.  See details... 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function downloads GEO SOFT files based on accession number.  It
does not do any parsing.  The first two arguments should be fairly
self-explanatory, but the last is based on the input to the acc.cgi
url at the geo website.  In the default "full" mode, the entire SOFT
format file is downloaded.  Both "brief" and "quick" offer shortened
versions of the files, good for "peeking" at the file before a big
download on a slow connection.  Finally, "data" downloads only the
data table part of the SOFT file and is good for downloading a simple
EXCEL-like file for use with other programs (a convenience).
\end{Details}
\begin{Value}
Invisibly returns the full path of the downloaded file.
\end{Value}
\begin{Author}\relax
Sean Davis
\end{Author}
\begin{References}\relax
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{getGEO}{getGEO}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  myfile <- getGEOfile('GDS2')
\end{ExampleCode}
\end{Examples}