[BioC] help with genotyping

[Benilton Carvalho]

there is a calls() accessor that will return you the calls as integers
(1: AA; 2: AB; 3: BB). So, something along the lines of:

theCalls = calls(object)
final = theCalls
for (i in 1:3)
   final[theCalls == i] = c('AA', 'AB', 'BB')[i]

Then it's just a matter of using write.table() to write out the file
using the "final" object.

b

On 13 July 2012 11:22, Pina Iannelli <pina.iannelli at gmail.com> wrote:
> Dear all,
> I run this code to get genotyping from Affymetrix SNP 6.0 arrays:
>
> fullFilenames <-
> list.celfiles("C:/Users/Pina/Bioinformatica/SNP/COR354_SNP6", full.names =
> TRUE)
> outputDir <- file.path(getwd(), "crlmmResults")
> exampleSet <- genotype(fullFilenames, batch = rep("1", 2), cdfName =
> "genomewidesnp6", gender=c(1, 2))
>
> Now I nead to ha ve a file with genotyping information, such as:
>
>    SNP_A-1780270 BB BB AA  SNP_A-1780272 BB AB BB
> How can I do it?
> Thanks for your help, best regards
> Pina
>
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