\HeaderA{cghRaw}{Class to contain and describe raw or normalized array comparative genomic hybridization data.}{cghRaw}
\aliasA{bpend,cghRaw-method}{cghRaw}{bpend,cghRaw.Rdash.method}
\aliasA{bpstart,cghRaw-method}{cghRaw}{bpstart,cghRaw.Rdash.method}
\aliasA{cghRaw-class}{cghRaw}{cghRaw.Rdash.class}
\aliasA{chromosomes,cghRaw-method}{cghRaw}{chromosomes,cghRaw.Rdash.method}
\aliasA{class:cghRaw}{cghRaw}{class:cghRaw}
\aliasA{copynumber,cghRaw-method}{cghRaw}{copynumber,cghRaw.Rdash.method}
\aliasA{copynumber<-,cghRaw,matrix-method}{cghRaw}{copynumber<.Rdash.,cghRaw,matrix.Rdash.method}
\aliasA{initialize,cghRaw-method}{cghRaw}{initialize,cghRaw.Rdash.method}
\aliasA{plot.cghRaw,cghRaw,missing-method}{cghRaw}{plot.cghRaw,cghRaw,missing.Rdash.method}
\keyword{classes}{cghRaw}
\begin{Description}\relax
Container for aCGH data and experimental
metadata. \code{cghRaw} class is derived from
\code{\LinkA{eSet}{eSet}}, and requires a matrix named \code{copynumber} as
assayData member. 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('cghRaw',
    phenoData = [AnnotatedDataFrame],
    experimentData = [MIAME],
    annotation = [character],
    copynumber = [matrix],
    featureData = [AnnotatedDataFrame],
    ...)
  }

\code{make\_cghRaw} is a function to convert a dataframe or textfile to
an object of class \code{cghRaw}. The input should be either a dataframe 
or a tabseparated textfile (textfiles must contain a header). The first 
three columns should contain the name, chromosome and position in bp for 
each array target respectively. The chromosome and position column must 
contain numbers only. Following these is a column with log2 ratios for 
each of your samples. If the input type is a textfile, missing values 
should be represented as 'NA' or an empty field.
\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{copynumber} 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(cghRaw)}, \code{copynumber(cghRaw,matrix)<-}] Access and
set elements named \code{copynumber} in the \code{AssayData-class}
slot.
\item[\code{chromosomes}, \code{bpstart}, \code{bpend}] Access the chromosomal positions stored in \code{featureData}
\item[plot.cghRaw] Create a plot containing log2ratios ordered by chromosomal position
}

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-class}{eSet.Rdash.class}}, \code{\LinkA{cghSeg-class}{cghSeg.Rdash.class}}, \code{\LinkA{cghCall-class}{cghCall.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        # create an instance of cghRaw
        new("cghRaw")
        
        # create an instance of cghRaw from a dataframe
        data(WiltingData)
        cghobj <- cghRaw(WiltingData)
        
        # plot the first sample
        plot.cghRaw(cghobj[,1])
        # first three chromosomes
        plot.cghRaw(cghobj[chromosomes(cghobj)==1,1])
        
        # get the copynumber values of the third and fourth sample
        log2ratios <- copynumber(cghobj[,3:4])
        
        # get the names of the samples
        sampleNames(cghobj)
        
        # get the names of the array elements
        featureNames(cghobj)
\end{ExampleCode}
\end{Examples}

