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

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

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
  }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(snapCGH)
Loading required package: limma
Loading required package: DNAcopy
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/snapCGH/convert.output.Rd_%03d_medium.png", width=480, height=480)
> ### Name: convert.output
> ### Title: Converts the output from the simulation to a format which can be
> ###   used by segmentation schemes available within R
> ### Aliases: convert.output
> ### Keywords: datasets
> 
> ### ** 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]]$genes) <- c("kb", "Chrom")
+     holder[[i]] <- new("aCGHList", holder[[i]])
+   }
+   holder
+   }
function (input) 
{
    holder <- list()
    for (i in 1:length(input)) {
        holder[[i]] <- list()
    }
    for (i in 1:length(input)) {
        holder[[i]]$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
}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>