[BioC] genotyping output files

[Vincent Carey]

Dear Rafiq S.

You do not have to reissue your query.  You can verify that it was
broadcast by checking the mailing list archive.

There are to my knowledge no immediate translations from crlmm output
to plink input.  The "downstream" vignette

http://www.bioconductor.org/packages/2.9/bioc/vignettes/crlmm/inst/doc/crlmmDownstream.pdf

shows some relevant conversions, but the document is obsolete and
needs to be rebuilt.  If you substitute "snpStats" for
"snpMatrix" and "SnpMatrix" for "snp.matrix", everything should work
as noted.  You can use coercion of the SnpMatrix instance to
"character" to get the calls in "A/B" format.

On Sat, Jan 14, 2012 at 6:42 PM, 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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