setupGADAIllumina: Imports Illumina array data to gada

Description Usage Arguments Details Value References See Also Examples

Description

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

Usage

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

Arguments

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

Details

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

Value

An object of class 'setupGADA'

References

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

See Also

setupGADAgeneral, setupGADAaffy

Examples

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## 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)


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