readAffybatchPara: Parallelized Read-AffyBatch function

In affyPara: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Description

Parallelization of the read.affybatch function. This parallel implementation is especially useful for multicore machines.

Usage

read.affybatchPara(object,
		phenoData = new("AnnotatedDataFrame"),
		description = NULL, notes = "",	
		cluster, verbose=getOption("verbose"), cdfname) 

Arguments

object	An object of a character vector with the names of CEL files OR a (partitioned) list of character vectors with CEL file names.
phenoData	An AnnotatedDataFrame object.
description	a 'MIAME' object.
notes	notes.
cluster	A cluster object obtained from the function makeCluster in the SNOW package. For default .affyParaInternalEnv$cl will be used.
verbose	A logical value. If TRUE it writes out some messages. default: getOption("verbose")
cdfname	cdfname to pass to the AffyBatch call

Details

Parallelized creation of an AffyBatch object. Especially useful on multi-core machines to accelerate the creation of the AffyBatch object.

For the serial function and more details see the function read.affybatch.

For using this function a computer cluster using the SNOW package has to be started. Starting the cluster with the command makeCluster generates an cluster object in the affyPara environment (.affyParaInternalEnv) and no cluster object in the global environment. The cluster object in the affyPara environment will be used as default cluster object, therefore no more cluster object handling is required. The makeXXXcluster functions from the package SNOW can be used to create an cluster object in the global environment and to use it for the preprocessing functions.

Value

An AffyBatch object.

Author(s)

Markus Schmidberger [e-mail], Ulrich Mansmann [e-mail]

Examples

## Not run: 
library(affyPara)
if (require(affydata)) {
	celpath <- system.file("celfiles", package="affydata")
    fns <- list.celfiles(path=celpath,full.names=TRUE)

	makeCluster(3)
	
	##read a text celfile
   	abatch <- read.affybatchPara(fns[2], verbose=TRUE)
	
	stopCluster()
}

## End(Not run)

affyPara documentation built on Nov. 8, 2020, 11:08 p.m.