\name{AffySNPCNVPDInfoPkgSeed2-class}
\Rdversion{1.1}
\docType{class}
\alias{AffySNPCNVPDInfoPkgSeed2-class}
%% \alias{chipName,AffySNPCNVPDInfoPkgSeed2-method}
%% \alias{makePdInfoPackage,AffySNPCNVPDInfoPkgSeed2-method}

\title{Class "AffySNPCNVPDInfoPkgSeed2"}
\description{A generic annotation package builder for Affymetrix SNP/CNV
  arrays. This is a simplified version of the annotation package and
  \code{crlmm} will *NOT* work for them.}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("AffySNPCNVPDInfoPkgSeed2", csvAnnoFileCnv, csvSeqFileCnv, ...)}.
}

\section{Slots}{
  \describe{
    \item{\code{cdfFile}:}{Path to the CDF file for this.}
    \item{\code{csvAnnoFile}:}{Path to the Affymetrix CSV annotation for
      the SNP probes.}
    \item{\code{csvSeqFile}:}{Path to the (SNP) probe sequence file.}
    \item{\code{csvAnnoFileCnv}:}{Path to the Affymetrix CSV annotation
      for the CNV probes.}
    \item{\code{csvSeqFileCnv}:}{Path to the (CNV) probe sequence file.}
    \item{\code{chipName}:}{Name of the chip or platform}
    \item{\code{manufacturer}:}{chip/platform manufacturer}
    \item{\code{url}:}{chip URL}
    \item{\code{genomebuild}:}{The genome build this platform is based
      upon.}
    \item{\code{organism}:}{ organism for chip. }
    \item{\code{species}:}{ species for chip. }  
    \item{\code{version}:}{A character vector giving the version
    number of the package.}
    \item{\code{license}:}{The license of the package}
    \item{\code{author}:}{Author of the package}
    \item{\code{email}:}{An email address to use in the Maintainer field}
    \item{\code{biocViews}:}{Character data for the biocViews field of
      the DESCRIPTION file}
  }
}
\section{Methods}{
  \describe{
    \item{chipName}{\code{signature(object = "AffySNPCNVPDInfoPkgSeed2")}: ... }
    \item{makePdInfoPackage}{\code{signature(object = "AffySNPCNVPDInfoPkgSeed2")}: ... }
	 }
}
\author{Benilton Carvalho}

\note{
  This is a simplified annotation package. CRLMM won't work for these
  objects.

  The user may need to rename the columns or even add column names to
  the annotation and sequence files. In case problems are found, column
  names are suggested.
  }

\examples{
showClass("AffySNPCNVPDInfoPkgSeed2")
}
\keyword{classes}