\name{getGEOfile}
\alias{getGEOfile}
\title{ Download a file from GEO soft file to the local machine }
\description{
  This function simply downloads a SOFT format file associated with the
  GEO accession number given.
}
\usage{
getGEOfile(GEO, destdir = tempdir(), AnnotGPL = FALSE, amount = c("full", "brief", "quick", "data"))
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{GEO}{Character string, the GEO accession for download (eg.,
    GDS84, GPL96, GSE2553, or GSM10)}
  \item{destdir}{Directory in which to store the resulting downloaded
    file.  Defaults to tempdir()}
  \item{AnnotGPL}{A boolean defaulting to FALSE as to whether or not to
    use the Annotation GPL information.  These files are nice to use
    because they contain up-to-date information remapped from Entrez
    Gene on a regular basis.  However, they do not exist for all GPLs;
    in general, they are only available for GPLs referenced by a GDS}
  \item{amount}{Amount of information to pull from GEO.  Only applies to
    GSE, GPL, or GSM.  See details... }
}
\details{
  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).
}
\value{
  Invisibly returns the full path of the downloaded file.
}
\references{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi}
\author{Sean Davis}
\seealso{\code{\link{getGEO}}}
\examples{
  # myfile <- getGEOfile('GDS10')
}

\keyword{ IO }