setupGADAIllumina: Imports Illumina array data to gada
In gada: Genome Alteration Detection Algorithm (GADA)

Description Usage Arguments Details Value References See Also Examples

This function encapsulates information obtained from Illumina platform (BeadStudio format) to be analyzed with gada

1	setupGADAIllumina(file, NumCols, log2ratioCol, MarkerIdCol = 1, ChrNameCol = 2, ChrPosCol = 3, XY=TRUE, sort = TRUE, orderProbes, saveGenInfo = TRUE)

`file`	A file with Illumina data (obtained from BeadStudio)
`NumCols`	The number of columns in 'file'
`log2ratioCol`	The column in 'file' containing log2ratio intensities
`MarkerIdCol`	The column in 'file' containing the name of the marker
`ChrNameCol`	The column in 'file' containing the chromosome
`ChrPosCol`	The column in 'file' containing the genomic position
`XY`	Do data have X and Y labels in annotation or 23 and 24? The default is TRUE
`sort`	Should data be sorted using annotation data? The default is TRUE
`orderProbes`	Used when sort is TRUE. See details
`saveGenInfo`	Should annotation data be saved? The default is TRUE. See details

The arguments 'orderProbes' and 'saveGenInfo' should not be changed by the user.

An object of class 'setupGADA'

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples", BMC Bioinformatics , Submitted Nov 2009

setupGADAgeneral, setupGADAaffy

## Not run: 
# get data
download.file("http://www.creal.cat/jrgonzalez/GADA/dataIllumina.txt",
               "./dataIllumina.txt")

dataIllumina<-setupGADAIllumina(file="dataIllumina.txt",log2ratioCol=5,NumCols=6)
dataIllumina

## End(Not run)