\name{convert.output}
\alias{convert.output}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Converts the output from the simulation to a format which can be used by segmentation schemes available within R }
\description{
  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.
}
\usage{
convert.output(input)
}
\arguments{
  \item{input}{ The output obtained upon applying the sim.structure function }
}
\details{
  This function outputs an object which is similar in structure/format to an RG or MA object used in Limma.
}
\value{
  This function outputs a list with entries
  \item{M }{A matrix containing the \eqn{\log_2} ratios}
  \item{genes }{A matrix containing the simulated midpoints and the chromosome which forms the template upon which the simulation is based.}
}
\author{ Michael Smith, John Marioni }

\examples{
## 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
  }
}
\keyword{ datasets }