[BioC] GWAS with Affymetrix SNP 6.0

[David Hervás]

Hello,

I'm new to Bioconductor and after searching and reading lots of documentation files from different packages I still haven't figured how to perform GWAS with Affymetrix SNP 6.0 arrays
As far as I know I need "oligo", "pd.genomewidesnp.6" and "snpStats" pacakages but I haven't found an example of how to put all the commands together.


I've managed to read my .CEL files with the following code provided in the oligo package documentation:

setwd("d:\\CELS\\")
fullFilenames <- list.celfiles(full.names=TRUE)    
outputDir <- file.path(getwd(), "crlmmResults")        

if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir)

crlmmOut <- getCrlmmSummaries(outputDir)


I get a SnpSuperSet object, and I also know how to get the genotypes from it with

genotype<-calls(crlmmOut)

What are the next steps to perform the association analysis? Documentation in oligo package suggests "snpStats" but I have no idea how to make this package read my SnpSuperSet object or my genotype matrix, since snpStats needs a SNPmatrix object. I've also tried other packages but none seem to be able to read SnpSuperSet objects. 

Thanks in advance for you help


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David Hervás Marín
Biostatistician in IIS La Fe - Valencia