\HeaderA{cghRegions}{Class to contain and describe array comparative genomic hybridization regions data.}{cghRegions}
\aliasA{avedist,cghRegions-method}{cghRegions}{avedist,cghRegions.Rdash.method}
\aliasA{bpend,cghRegions-method}{cghRegions}{bpend,cghRegions.Rdash.method}
\aliasA{bpstart,cghRegions-method}{cghRegions}{bpstart,cghRegions.Rdash.method}
\aliasA{cghRegions-class}{cghRegions}{cghRegions.Rdash.class}
\aliasA{chromosomes,cghRegions-method}{cghRegions}{chromosomes,cghRegions.Rdash.method}
\aliasA{class:cghRegions}{cghRegions}{class:cghRegions}
\aliasA{frequencyPlot,cghRegions,missing-method}{cghRegions}{frequencyPlot,cghRegions,missing.Rdash.method}
\aliasA{initialize,cghRegions-method}{cghRegions}{initialize,cghRegions.Rdash.method}
\aliasA{nclone,cghRegions-method}{cghRegions}{nclone,cghRegions.Rdash.method}
\aliasA{plot.cghRegions,cghRegions,missing-method}{cghRegions}{plot.cghRegions,cghRegions,missing.Rdash.method}
\aliasA{regions,cghRegions-method}{cghRegions}{regions,cghRegions.Rdash.method}
\aliasA{regions<-,cghRegions,matrix-method}{cghRegions}{regions<.Rdash.,cghRegions,matrix.Rdash.method}
\keyword{classes}{cghRegions}
\begin{Description}\relax
Container for aCGH regions data and experimental
metadata. \code{cghRegions} class is derived from
\code{\LinkA{eSet}{eSet}}, and requires a matrix named \code{regions} as
assayData member. Furthermore, columns named \code{Chromosome}, \code{Start}, \code{End},
\code{Nclone}, and \code{Avedist} are required as featureData members, containing region 
and position information.
\end{Description}
\begin{Section}{Extends}
Directly extends class \code{\LinkA{eSet}{eSet}}.
\end{Section}
\begin{Section}{Creating Objects}
\code{new('cghRegions',
    phenoData = [AnnotatedDataFrame],
    experimentData = [MIAME],
    annotation = [character],
    regions = [matrix],
    featureData = [AnnotatedDataFrame],
    ...)
  }

An object of this class is generally obtained by running the function \code{\LinkA{CGHregions}{CGHregions}}.
\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 a matrix
\code{regions} with rows represening regions
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}{AssayData}}
\item[\code{phenoData}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{featureData}:] An \code{\LinkA{AnnotatedDataFrame}{AnnotatedDataFrame}} with columns
\code{Chromosome}, \code{Start}, \code{End}, \code{Nclone}, and \code{Avedist} containing region 
and position information.
\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{regions(cghRegions)}, \code{regions(cghRegions,matrix)<-}] Access and
set elements named \code{regions} in the \code{AssayData-class}
slot.
\item[\code{chromosomes}, \code{bpstart}, \code{bpend}, \code{nclone}, \code{avedist}] Access the region and position
information stored in \code{featureData}
\item[plot.cghRegions] Create a plot displaying chromosomes on the Y-axis and base pair position on the X-axis. A new region is displayed by a slight jump with respect to the previous region. Each region is displayed as a bi-colored segment, the lower and upper part of which correspond to the proportions pl and pg of samples with a loss (red) or gain (green), respectively. The color coding is displayed as well: 1: pl (pg) \textless{} 10\%; 2: 10\% = pl (pg) \textless{} 30\%; 3:30\% = pl (pg) \textless{} 50\%; 4: pl (pg) = 50\%.
\item[frequencyPlot] Create a frequency plot
}

See \code{\LinkA{eSet}{eSet}} for derived methods. Annotation functionality is not yet supported.
\end{Section}
\begin{Author}\relax
Sjoerd Vosse
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{eSet}{eSet}}, \code{\LinkA{cghRaw}{cghRaw}}, \code{\LinkA{cghSeg}{cghSeg}}, \code{\LinkA{cghCall}{cghCall}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

        # create an instance of cghRegions
        new("cghRegions")
        
        # load an instance of cghRegions
        data(WiltingRegions)
                
        # plot all region data
        plot.cghRegions(WiltingRegions)
        # make a frequency plot
        frequencyPlot(WiltingRegions)
        
        # extract the region values
        values <- regions(WiltingRegions)
        
        # get the names of the samples
        sampleNames(WiltingRegions)

\end{ExampleCode}
\end{Examples}

