\name{cghSeg}
\docType{class}
\alias{class:cghSeg}
\alias{cghSeg}

\alias{cghSeg-class}

\alias{copynumber,cghSeg-method}
\alias{copynumber<-,cghSeg,matrix-method}
\alias{segmented,cghSeg-method}
\alias{segmented<-,cghSeg,matrix-method}

\alias{chromosomes,cghSeg-method}
\alias{bpstart,cghSeg-method}
\alias{bpend,cghSeg-method}

\alias{initialize,cghSeg-method}
\alias{plot.cghSeg,cghSeg,missing-method}

\title{
  Class to contain and describe segmented array comparative genomic hybridization data.
}

\description{
  Container for aCGH data and experimental
  metadata. \code{cghSeg} class is derived from
  \code{\link[Biobase:class.eSet]{eSet}}, and requires a matrix named \code{copynumber} as well as a 
  matrix named \code{segmented} as assayData members of equal dimensions. 
  Furthermore, columns named \code{Chromosome}, \code{Start}, and \code{End} are 
  required as featureData members, containing feature position information.
}
\section{Extends}{
   Directly extends class \code{\link[Biobase:class.eSet]{eSet}}.
}
\section{Creating Objects}{

  \code{new('cghSeg',
    phenoData = [AnnotatedDataFrame],
    experimentData = [MIAME],
    annotation = [character],
    copynumber = [matrix],
    segmented = [matrix],
    featureData = [AnnotatedDataFrame],
    ...)
  }

  An object of class \code{cghSeg} is generally obtained as output
  from \code{\link[CGHcall]{segmentData}}.

}
\section{Slots}{
  Inherited from \code{eSet}:
   \describe{
      \item{\code{assayData}:}{Contains matrices with equal
	dimensions, and with column number equal to
	\code{nrow(phenoData)}. \code{assayData} must contain matrices
	\code{copynumber} and \code{segmented} with rows represening array probes
	and columns representing samples. Additional matrices of
	identical size (e.g., representing measurement errors) may
	also be included in \code{assayData}. Class:\code{\link[Biobase:class.AssayData]{AssayData-class}}}
      \item{\code{phenoData}:}{See \code{\link[Biobase:class.eSet]{eSet}}}
      \item{\code{featureData}:}{An \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}} with columns
	\code{Chromosome}, \code{Start}, and \code{End} containing array element position 
	data.}
      \item{\code{experimentData}:}{See \code{\link[Biobase:class.eSet]{eSet}}}
      \item{\code{annotation}:}{See \code{\link[Biobase:class.eSet]{eSet}}}
  }
}
\section{Methods}{

  Class-specific methods.
  \describe{
     \item{\code{copynumber(cghSeg)}, \code{copynumber(cghSeg,matrix)<-}}{Access and
       set elements named \code{copynumber} in the \code{AssayData-class}
       slot.}
     \item{\code{segmented(cghSeg)}, \code{segmented(cghSeg,matrix)<-}}{Access and
       set elements named \code{segmented} in the \code{AssayData-class}
       slot.}
     \item{\code{chromosomes}, \code{bpstart}, \code{bpend}}{Access the chromosomal positions stored in \code{featureData}}
     \item{plot.cghSeg}{Create a plot containing log2ratios and segments ordered by chromosomal position}
    }

   See \code{\link[Biobase:class.eSet]{eSet}} for derived methods.   
}

\author{Sjoerd Vosse}

\seealso{
  \code{\link[Biobase:class.eSet]{eSet-class}},
  \code{\link[Biobase:class.ExpressionSet]{ExpressionSet-class}},
  \code{\link{cghRaw-class}}, \code{\link{cghCall-class}} 
}

\examples{

	# create an instance of cghSeg
	new("cghSeg")
	
	# load an instance of cghSeg
	data(WiltingSeg)

	# plot the first sample
	# plot.cghSeg(WiltingSeg[,1])
	# first three chromosomes
	# plot.cghSeg(WiltingSeg[chromosomes(WiltingSeg)==1,1])
	
	# get the copynumber values of the third and fourth sample
	log2ratios <- copynumber(WiltingSeg[,3:4])
	
	# get the names of the samples
	sampleNames(WiltingSeg)
	
	# get the names of the array elements
	featureNames(WiltingSeg)

}

\keyword{classes}