\HeaderA{cghCall}{Class to contain and describe called array comparative genomic hybridization data.}{cghCall}
\aliasA{bpend,cghCall-method}{cghCall}{bpend,cghCall.Rdash.method}
\aliasA{bpstart,cghCall-method}{cghCall}{bpstart,cghCall.Rdash.method}
\aliasA{calls,cghCall-method}{cghCall}{calls,cghCall.Rdash.method}
\aliasA{calls<-,cghCall,matrix-method}{cghCall}{calls<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{cghCall-class}{cghCall}{cghCall.Rdash.class}
\aliasA{chromosomes,cghCall-method}{cghCall}{chromosomes,cghCall.Rdash.method}
\aliasA{class:cghCall}{cghCall}{class:cghCall}
\aliasA{copynumber,cghCall-method}{cghCall}{copynumber,cghCall.Rdash.method}
\aliasA{copynumber<-,cghCall,matrix-method}{cghCall}{copynumber<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{initialize,cghCall-method}{cghCall}{initialize,cghCall.Rdash.method}
\aliasA{plot.cghCall,cghCall,missing-method}{cghCall}{plot.cghCall,cghCall,missing.Rdash.method}
\aliasA{probamp,cghCall-method}{cghCall}{probamp,cghCall.Rdash.method}
\aliasA{probamp<-,cghCall,matrix-method}{cghCall}{probamp<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{probgain,cghCall-method}{cghCall}{probgain,cghCall.Rdash.method}
\aliasA{probgain<-,cghCall,matrix-method}{cghCall}{probgain<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{probloss,cghCall-method}{cghCall}{probloss,cghCall.Rdash.method}
\aliasA{probloss<-,cghCall,matrix-method}{cghCall}{probloss<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{probnorm,cghCall-method}{cghCall}{probnorm,cghCall.Rdash.method}
\aliasA{probnorm<-,cghCall,matrix-method}{cghCall}{probnorm<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{segmented,cghCall-method}{cghCall}{segmented,cghCall.Rdash.method}
\aliasA{segmented<-,cghCall,matrix-method}{cghCall}{segmented<.Rdash.,cghCall,matrix.Rdash.method}
\aliasA{summaryPlot,cghCall,missing-method}{cghCall}{summaryPlot,cghCall,missing.Rdash.method}
\keyword{classes}{cghCall}
\begin{Description}\relax
Container for aCGH data and experimental
metadata. \code{cghCall} class is derived from
\code{\LinkA{eSet}{eSet}}, and requires the following matrices of equal dimension
as assayData members:
\Itemize{
\item \code{copynumber} Log2 copynumber ratios.
\item \code{segmented}  Segmented log2 ratios.
\item \code{calls}                Called copynumer values.
\item \code{probloss}           Loss probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}}.
\item \code{probnorm}           Normal probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}}.
\item \code{probgain}           Gain probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}}.
\item \code{probamp}            Optional amplification probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}} when run with \code{nclass=4}.
}
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('cghCall',
    phenoData = [AnnotatedDataFrame],
    experimentData = [MIAME],
    annotation = [character],
    copynumber = [matrix],
    segmented = [matrix],
    calls = [matrix],
    probloss = [matrix],
    probnorm = [matrix],
    probgain = [matrix],
    featureData = [AnnotatedDataFrame],
    ...)
  }

An object of class \code{cghCall} is generally obtained as output
from \code{\LinkA{CGHcall}{CGHcall}}.
\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 the following matrices
\Itemize{
\item \code{copynumber} Log2 copynumber ratios.
\item \code{segmented}  Segmented log2 ratios.
\item \code{calls}                Called copynumer values.
\item \code{probloss}           Loss probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}}.
\item \code{probnorm}           Normal probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}}.
\item \code{probgain}           Gain probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}}.
\item \code{probamp}            Optional amplification probabilities as returned by \code{\LinkA{CGHcall}{CGHcall}} when run with \code{nclass=4}.
}     
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(cghCall)}, \code{copynumber(cghCall,matrix)<-}] Access and
set elements named \code{copynumber} in the \code{AssayData-class}
slot.
\item[\code{segmented(cghCall)}, \code{segmented(cghCall,matrix)<-}] Access and
set elements named \code{segmented} in the \code{AssayData-class}
slot.
\item[\code{calls(cghCall)}, \code{calls(cghCall,matrix)<-}] Access and
set elements named \code{calls} in the \code{AssayData-class}
slot.
\item[\code{probloss(cghCall)}, \code{probloss(cghCall,matrix)<-}] Access and
set elements named \code{probloss} in the \code{AssayData-class}
slot.
\item[\code{probnorm(cghCall)}, \code{probnorm(cghCall,matrix)<-}] Access and
set elements named \code{probnorm} in the \code{AssayData-class}
slot.
\item[\code{probgain(cghCall)}, \code{probgain(cghCall,matrix)<-}] Access and
set elements named \code{probgain} in the \code{AssayData-class}
slot.
\item[\code{chromosomes}, \code{bpstart}, \code{bpend}] Access the chromosomal positions stored in \code{featureData}
\item[plot.cghCall] Create a plot containing log2ratios, segments and call probabilities ordered by chromosomal position
\item[summaryPlot] Create a plot summarizing the call probabilities of all samples
}

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{cghSeg-class}{cghSeg.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

        # create an instance of cghCall
        new("cghCall")
        
        # load an instance of cghCall
        data(WiltingCalled)
  
  # plot the first sample
  plot.cghCall(WiltingCalled[,1])
  
  # plot the first chromosome of the first sample
  plot.cghCall(WiltingCalled[chromosomes(WiltingCalled)==1,1])

  # get the copynumber values of the third and fourth sample
  log2ratios <- copynumber(WiltingCalled[,3:4])

  # get the names of the samples
  sampleNames(WiltingCalled)

  # get the names of the array elements
  featureNames(WiltingCalled)

\end{ExampleCode}
\end{Examples}

