\HeaderA{convert.output}{Converts the output from the simulation to a format which can be used by segmentation schemes available within R}{convert.output}
\keyword{datasets}{convert.output}
\begin{Description}\relax
This function converts the output obtained by applying our simulation scheme into a format that can be used (either directly or indirectly) as the input to various segmentation schemes available within R. Additionally, we are in the process of submitting a library to CRAN which will enable the user to apply a number of the segmentation schemes available within R to datasets which have the same structure as that generated by this function.
\end{Description}
\begin{Usage}
\begin{verbatim}
convert.output(input)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{input}] The output obtained upon applying the sim.structure function 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function outputs an object which is similar in structure/format to an RG or MA object used in Limma.
\end{Details}
\begin{Value}
This function outputs a list with entries
\begin{ldescription}
\item[\code{M }] A matrix continaing the $\mbox{log}_2$ ratios
\item[\code{genes }] A matrix containing the simulated midpoints and the chromosome which forms the template upon which the simulation is based.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Michael Smith, John Marioni
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## The function is currently defined as
function(input){
  holder <- list()
  for (i in 1:length(input)){
  holder[[i]] <- list()}
  for(i in 1:length(input)){
    holder[[i]]$genes <- matrix(NA, nrow = length(input[[i]]$clones$mid.point),
                                ncol = 2)
  }
  for(i in 1:length(input)){
    holder[[i]]$M <- as.matrix(input[[i]]$datamatrix)
    holder[[i]]$genes[,1] <- input[[i]]$clones$mid.point
    holder[[i]]$genes[,2] <- rep(input[[i]]$chrom,length(input[[i]]$clones$mid.point))
    colnames(holder[[i]]$genes) <- c("kb", "Chrom")
    holder[[i]] <- new("aCGHList", holder[[i]])
  }
  holder
  }
\end{ExampleCode}
\end{Examples}

