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

\alias{cghCall-class}

\alias{copynumber,cghCall-method}
\alias{copynumber<-,cghCall,matrix-method}
\alias{segmented,cghCall-method}
\alias{segmented<-,cghCall,matrix-method}
\alias{calls,cghCall-method}
\alias{calls<-,cghCall,matrix-method}
\alias{probloss,cghCall-method}
\alias{probloss<-,cghCall,matrix-method}
\alias{probnorm,cghCall-method}
\alias{probnorm<-,cghCall,matrix-method}
\alias{probgain,cghCall-method}
\alias{probgain<-,cghCall,matrix-method}
\alias{probamp,cghCall-method}
\alias{probamp<-,cghCall,matrix-method}

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

\alias{initialize,cghCall-method}
\alias{plot,cghCall,missing-method}
\alias{plot.summary,cghCall,missing-method}

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

\description{
  Container for aCGH data and experimental
  metadata. \code{cghCall} class is derived from
  \code{\link[Biobase]{eSet}}, and requires the following matrices of equal dimension
  as assayData members:
  \itemize{
    \item \code{copynumber}
    \item \code{segmented}
    \item \code{calls}
    \item \code{probloss}
    \item \code{probnorm}
    \item \code{probgain}
  }
  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]{eSet}}.
}
\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{\link{CGHcall}}.

}
\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}
        \item \code{segmented}
        \item \code{calls}
        \item \code{probloss}
        \item \code{probnorm}
        \item \code{probgain}
    }   
    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]{AssayData-class}}}
      \item{\code{phenoData}:}{See \code{\link[Biobase]{eSet}}}
      \item{\code{featureData}:}{An \code{\link[Biobase]{AnnotatedDataFrame}} with columns
    \code{Chromosome}, \code{Start}, and \code{End} containing array element position 
    data.}
      \item{\code{experimentData}:}{See \code{\link[Biobase]{eSet}}}
      \item{\code{annotation}:}{See \code{\link[Biobase]{eSet}}}
  }
}
\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}{Create a plot containing log2ratios, segments and call probabilities ordered by chromosomal 
     position. TWO EXTRA OPTIONS PLUS DEFAULTS: 
     dotres=10. Every dotres-th log2-ratio is plotted. dotres=1 plots all data. However, higher values save a lot of space and 
     allow quicker browsing of the plots. ylimit=c(-5,5): limits of the y-axis}
     \item{plot.summary}{Create a plot summarizing the call probabilities of all samples}
    }

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

\author{Sjoerd Vosse}

\seealso{
  \code{\link[Biobase]{eSet-class}}, \code{\link{cghRaw-class}}, \code{\link{cghSeg-class}}
}

\examples{
# create an instance of cghCall
new("cghCall")

# create an instance of cghCall through \code{\link{ExpandCGHcall}}
\dontrun{
   data(Wilting)
   rawcgh <- make_cghSeg(Wilting)
   normalized <- normalize(rawcgh)
   segmented <- segmentData(normalized)
   listcalled <- CGHcall(segmented)
   called <- ExpandCGHcall(listcalled,segmented)

   # plot the first sample. Default only every 10th log2-ratio is plotted (dotres=10). Adjust using dotres= option below. 
   plot(called[,1])
   # plot the first chromosome of the first sample
   plot(called[chromosomes(called)==1,1])

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

   # get the names of the samples
   sampleNames(called)

   # get the names of the array elements
   featureNames(called)
}
}
\keyword{classes}