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

\alias{cghRaw-class}

\alias{copynumber,cghRaw-method}
\alias{copynumber<-,cghRaw,matrix-method}

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

\alias{initialize,cghRaw-method}
\alias{plot.cghRaw,cghRaw,missing-method}

\title{
  Class to contain and describe raw or normalized array comparative genomic hybridization data.
}

\description{
  Container for aCGH data and experimental
  metadata. \code{cghRaw} class is derived from
  \code{\link[Biobase:class.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.
}
\section{Extends}{
   Directly extends class \code{\link[Biobase:class.eSet]{eSet}}.
}
\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.

}
\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{\link[Biobase:class.AssayData]{AssayData-class}}}
      \item{\code{phenoData}:}{See \code{\link[Biobase:class.eSet]{eSet}}}
      \item{\code{featureData}:}{An \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}} with columns
	\code{Chromosome}, \code{Start}, and \code{End} containing array element position 
	data.}
      \item{\code{experimentData}:}{See \code{\link[Biobase:class.eSet]{eSet}}}
      \item{\code{annotation}:}{See \code{\link[Biobase:class.eSet]{eSet}}}
  }
}
\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{\link[Biobase:class.eSet]{eSet}} for derived methods. Annotation functionality is not yet supported.   
}

\author{Sjoerd Vosse}

\seealso{
  \code{\link[Biobase:class.eSet]{eSet-class}}, \code{\link{cghSeg-class}}, \code{\link{cghCall-class}}
}

\examples{
	# 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)
}
\keyword{classes}