\name{getGEOSAGE}
\alias{getGEOSAGE}
\alias{getFileNames}
\alias{getSampleId}
\alias{parseSAGE}

\title{Automatically downloads SAGE libraries from NCBI}
\description{
  Given an organism name (e.g. human) and a correct url,
  \code{\link{getGEOSAGE}} downloads SAGE libraries and stores them in a
  specified directory
}
\usage{
getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url =
"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
getFileNames(organism, url)
getSampleId(url)
}

\arguments{
  \item{organism}{A character string for the name of the organism of
    interests}
  \item{targetDir}{A character string for the directory where the
    downloaded SAGE libraries will be stored}
  \item{quiet}{A boolean indicating whether the status message from
    \code{\link{download.file}} will be supressed}
  \item{url}{A character string for part of the url from which SAGE libraries
    will be downloaded}
}
\details{
  \code{\link{getGEOSAGE}} downloads SAGE libraries from NCBI's GEO site
  and stores them in a specified directory. The url passed is the
  location where the cgi resides and will be appended the correct
  parameters that specifies the content and format of the data file to
  be downloaded.

  The system relies on GPL numbers that differ among organisms to find
  the correct platform sample ids for files belonging to a given
  organism. The platform sample ids will then be used to fetch the
  desired annotation files. \code{\link{getFileNames}} gets the correct
  GPL number and \code{\link{getSampleId}} gets the platform sample
  ids. \code{\link{parseSAGE}} parses the downloaded file and stores the
  data to a specified place.   
}
\value{
  \item{getFileNames}{Returns a vector of GPL numbers}
  \item{getSampleId}{Returns a vector of platform sample ids}
}
\references{\url{http://www.ncbi.nlm.nih.gov/geo/query/}}
\author{J. Zhang}

\seealso{\code{\link{mergeSAGE}}}

\examples{
# Since downloading and parsing SAGE libraries are time consuming, the
# example code is inactivated.
\dontrun{getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url =
"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")}  
}
\keyword{manip}