convert.output: Converts the output from the simulation to a format which can...

In snapCGH: Segmentation, normalisation and processing of aCGH data

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
  }

Example output

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
}

snapCGH documentation built on Nov. 8, 2020, 5:31 p.m.