[BioC] genotyping output files

[Benilton Carvalho]

simply get the output of calls(crlmmResult), for example:

theCalls = calls(crlmmResult)

and write it out to a text file:

write.table(theCalls, file='theCalls.txt', sep='\t', quote=FALSE)

and this will create a tab-delimited file in which the rows are the
SNPs and the columns are the samples.

Note that the calls are coded 1 (AA), 2 (AB) and 3 (BB)...

b

On 14 January 2012 23:42, Rafiq S. <S.Rafiq at soton.ac.uk> wrote:
>
> Dear All,
>
> I have recently attempted a genome wide genotyping experiment on around 500 samples using the Illumina 660quad chip.
> Crlmm genotyping was completed and a snpset object crlmmResult was created.
>
> I have used the calls(crlmmResult) and the configuation command to quickly browse through the genotypes.
>
> I was expecting that at the end of the process crlmm would produce a text file with all the genotypes which could be transported to other softwares like plink for association analysis,
> This hasnt happened and a text file was not generated,  however a crlmmResult.Rda file was extracted into SNPchip packages in my rlibrary.
>
> Could you please direct  me towards what other prrocesses which I might  need to complete before I can obtain an output text file all the with genome wide calls?
>
> Many Thanks,
>
> -S
>
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