\HeaderA{cghSeg}{Class to contain and describe segmented array comparative genomic hybridization data.}{cghSeg}
\aliasA{bpend,cghSeg-method}{cghSeg}{bpend,cghSeg.Rdash.method}
\aliasA{bpstart,cghSeg-method}{cghSeg}{bpstart,cghSeg.Rdash.method}
\aliasA{cghSeg-class}{cghSeg}{cghSeg.Rdash.class}
\aliasA{chromosomes,cghSeg-method}{cghSeg}{chromosomes,cghSeg.Rdash.method}
\aliasA{class:cghSeg}{cghSeg}{class:cghSeg}
\aliasA{copynumber,cghSeg-method}{cghSeg}{copynumber,cghSeg.Rdash.method}
\aliasA{copynumber<-,cghSeg,matrix-method}{cghSeg}{copynumber<.Rdash.,cghSeg,matrix.Rdash.method}
\aliasA{initialize,cghSeg-method}{cghSeg}{initialize,cghSeg.Rdash.method}
\aliasA{plot.cghSeg,cghSeg,missing-method}{cghSeg}{plot.cghSeg,cghSeg,missing.Rdash.method}
\aliasA{segmented,cghSeg-method}{cghSeg}{segmented,cghSeg.Rdash.method}
\aliasA{segmented<-,cghSeg,matrix-method}{cghSeg}{segmented<.Rdash.,cghSeg,matrix.Rdash.method}
\keyword{classes}{cghSeg}
\begin{Description}\relax
Container for aCGH data and experimental
metadata. \code{cghSeg} class is derived from
\code{\LinkA{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.
\end{Description}
\begin{Section}{Extends}
Directly extends class \code{\LinkA{eSet}{eSet}}.
\end{Section}
\begin{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{\LinkA{segmentData}{segmentData}}.
\end{Section}
\begin{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{\LinkA{AssayData-class}{AssayData.Rdash.class}}
\item[\code{phenoData}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{featureData}:] An \code{\LinkA{AnnotatedDataFrame}{AnnotatedDataFrame}} with columns
\code{Chromosome}, \code{Start}, and \code{End} containing array element position 
data.
\item[\code{experimentData}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{annotation}:] See \code{\LinkA{eSet}{eSet}}
}
\end{Section}
\begin{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{\LinkA{eSet}{eSet}} for derived methods.
\end{Section}
\begin{Author}\relax
Sjoerd Vosse
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{eSet-class}{eSet.Rdash.class}}, \code{\LinkA{cghRaw-class}{cghRaw.Rdash.class}}, \code{\LinkA{cghCall-class}{cghCall.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

        # 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)

\end{ExampleCode}
\end{Examples}

