outputToCGHregions {ADaCGH2} | R Documentation

## ADaCGH2 output as input to CGHregions

### Description

Convert ADaCGH2 output to a data frame that can be used as input for `CGHregions`. This function takes as input the two possible types of input produced by the `pSegment` functions: either an ff object (and its associated directory) or the names of the RAM objects (the usual, in memory R objects) with the output, and chromosome, position, and probe name information.

### Usage

    outputToCGHregions(ffoutput = NULL, directory = getwd(),
                                   output.dat = NULL,
                                   chrom.dat = NULL,
                                   pos.dat = NULL,
                                   probenames.dat = NULL)

### Arguments

`ffoutput` | The name of the ff object with the output from a call to a `pSegment` function. You must provide either this argument or all of the arguments output.dat, chrom.dat, pos.dat and probenames.dat.
`directory` | The directory where the initial data transformation and the analysis have been carried out. It is a lot better if you just work on a single directory for a set of files. Otherwise, unless you keep very carefull track of where you do what, you will run into trouble. This is only relevant if you use an `ff` object (i.e., if `ffoutput` is not NULL.)
`output.dat` | The name of the RAM object with the output from a call to a `pSegment` function. You must provide this argument (as well as chrom.dat, pos.dat and probenames.dat) OR the name of an ffobject to argument `ffoutput.`
`chrom.dat` | The name of the RAM object with the chromosome data information. See the help for `inputToADaCGH`.
`pos.dat` | The name of the RAM object with the position data information. See the help for `inputToADaCGH`.
`probenames.dat` | The name of the RAM object with the probe names. See the help for `inputToADaCGH`.

### Value

A data frame of 4 + k columns that can be used as input to the `CGHregions` function. The first four columns are the probe name, the chromosome, the position and the position. The last k columns are the calls for the k samples.

### Note

This function does NOT check if the calls are meaningfull. In particular, you probably do NOT want to use this function when `pSegment` has been called using merging = "none".

Moreover, we do not check if there are missing values, and CGHregions is likely to fail when there are NAs. Finally, we do not try to use `ff` objects, so using this function with very large objects will probably fail.

### Author(s)

Ramon Diaz-Uriarte rdiaz02@gmail.com

### See Also

`pSegment`

### Examples

    ## Get location (and full filename) of example data file
    ## We will read from a text file

    fnametxt <- list.files(path = system.file("data", package = "ADaCGH2"),
                             full.names = TRUE, pattern = "inputEx.txt")

    ##################################
    #####
    ##### Using RAM objects
    #####
    ##################################

    ## Read data into RAM objects

    ##    You might want to adapt mc.cores to your hardware
    inputToADaCGH(ff.or.RAM = "RAM",
                  textfilename = fnametxt,
                  mc.cores = 2)

    ## Run segmentation (e.g., HaarSeg)

    ##    You might want to adapt mc.cores to your hardware
    haar.RAM.fork <- pSegmentHaarSeg(cgh.dat, chrom.dat,
                                     merging = "MAD",
                                     mc.cores = 2)

    forcghr <- outputToCGHregions(output.dat = haar.RAM.fork,
                                  chrom.dat = chrom.dat,
                                  pos.dat = pos.dat,
                                  probenames.dat = probenames.dat)

    ## Run CGHregions
    if(require(CGHregions)) {
      regions1 <- CGHregions(na.omit(forcghr))
      regions1
    }

    ##################################
    #####
    ##### Using ff objects
    #####
    ##################################

    if(.Platform$OS.type != "windows") {

    ## We do not want this to run in Windows the automated tests since
    ## issues with I/O. It should work, though, in interactive usage

    ## Create a temp dir for storing output.
    ## (Not needed, but cleaner).
    dir.create("ADaCGH2_cghreg_example_tmp_dir")
    originalDir <- getwd()
    setwd("ADaCGH2_cghreg_example_tmp_dir")
    ## Sys.sleep(1)

    ##    You might want to adapt mc.cores to your hardware
    inputToADaCGH(ff.or.RAM = "ff",
                  textfilename = fnametxt,
                  mc.cores = 2)

    ##    You might want to adapt mc.cores to your hardware
    haar.ff.fork <- pSegmentHaarSeg("cghData.RData",
                                    "chromData.RData",
                                    merging = "MAD",
                                    mc.cores = 2)

    forcghr.ff <- outputToCGHregions(ffoutput = haar.ff.fork)

    if(require(CGHregions)) {
      regions1 <- CGHregions(na.omit(forcghr.ff))
      regions1
    }

    ### Clean up (DO NOT do this with objects you want to keep!!!)
    load("chromData.RData")
    load("posData.RData")
    load("cghData.RData")

    delete(cghData); rm(cghData)
    delete(posData); rm(posData)
    delete(chromData); rm(chromData)
    unlink("chromData.RData")
    unlink("posData.RData")
    unlink("cghData.RData")
    unlink("probeNames.RData")

    lapply(haar.ff.fork, delete)
    rm(haar.ff.fork)

    ### Delete all files and temp dir
    setwd(originalDir)
    ## Sys.sleep(2)
    unlink("ADaCGH2_cghreg_example_tmp_dir", recursive = TRUE)
    ## Sys.sleep(2)
    }

[Package ADaCGH2 version 2.30.0 Index]