convert.output {snapCGH} | R Documentation

## 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

`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

`M` | A matrix containing the \log_2 ratios
`genes` | A matrix containing the simulated midpoints and the chromosome which forms the template upon which the simulation is based.

### Author(s)

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
      }

[Package snapCGH version 1.56.0 Index]