\name{readGenes}
\alias{readGenes}
\alias{genotypeFileFormats}
\alias{phenotypeFileFormats}
\alias{markerFileFormats}
\title{Import genetic data from standard file formats}
\description{ 
Import genetic data from standard file formats.
}
\usage{
readGenes(gfile, gformat=genotypeFileFormats,  goptions=list(),
          pfile, pformat=phenotypeFileFormats, poptions=list(),
          mfile, mformat=markerFileFormats,    moptions=list() )
}
\arguments{
  \item{gfile}{File containing genotype data}
  \item{gformat}{Function, function name, or a character file format
    specification from the list \code{genotypeFileFormats}.}
  \item{goptions}{Optional arguments for loading genotype data.}

  \item{pfile}{File containing phenotype data}
  \item{pformat}{Function, function name, or a character file format
    specification from the list \code{phenotypeFileFormats}.}
  \item{poptions}{Optional arguments for loading phenotype data.}

  \item{mfile}{File containing marker data}
  \item{mformat}{Function, function name, or a character file format
    specification from the list \code{markerFileFormats}.}
  \item{moptions}{Optional arguments for loading marker data.}
}
\details{
  Load genotype and (optionally) phenotype and marker information from the
  specified files and generate a geneSet object containing the
  results.

  A variety of file formats are available.  See the variables
  \code{genotypeFileFormats}, \code{phenotypeFileFormats},
  \code{phenotypeFileFormats} for formats.
}
\value{
  An object of class geneSet.
}
\author{Gregory R. Warnes \email{warnes@bst.rochester.edu} }
\note{
  Adding a new genotype (phenotype) file format requires creation of a
  function named \code{readGenes.newformat} (\code{read.newformat}) and
  adding the string "newformat" to the vector \code{genotypeFileFormats}
  (\code{phenotypeFileFormats}).

  Please submit new format functions to the authors for inclusion in the
  package.
}

\seealso{\code{\link{read.table}}, etc}
\examples{

# Perlegen data set (if we have access to it)
# (189K SNPS x 1008 patients)
path <- "~/clingen/Perlegen_Metabolic_Disorder/Data"
fname <- file.path(path,"PFZ_03/genotype.txt.gz")
if(file.exists(fname))
  {
    genef   <- gzfile(fname) # open the gzip compressed SNP file
    #phenof  <- 
    markerf <-file.path(path,"PFZ_03/snp_info.txt")
 
    pgdata <- readGenes(gfile=genef, gformat="perlegen",
                        mfile=markerf, mformat="table",
                        moptions=list(sep="\t",header=TRUE))
    close(genef)
  }


}
\keyword{misc}