[BioC] Converting Genotyping result for PLINK

[Claus-Jürgen Scholz]

Dear Peter,

I don't know a conversion package to create ped/map files as output.
However, the file format ist pretty straightforward (for a definition I
again recommend the excellent PLINK website, see
http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped) and even
without a converter it should be easy to create. For my annotations, I
once downloaded the SNP 6.0 annotation file from Affymetrix and simply
extracted relevant data from there. Otherwise, you can get annotation
online from Affymetrix NetAffx.
For the "numeric genotype code to genotype" conversion, first transpose
(using t() ) your results data frame so that SNPs are in columns. Then
coerce each column to a factor. Levels for this factor (retrieve with
levels() ) should then be "1", "2" and "3". Then replace the levels with
the genotypes ( e.g. levels(my.factor) <- c("A A","A B","B B"), or
rather with the SNP alleles from the annotation file), attach the
necessary pedigree information (see above) using cbind() and save as a
table. That's your ped file. For the map file, extract chromosome
position and rs number from the annotation file and save it in the
format described  in
http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#map

Cheers,
CJ


Peter Ganske schrieb:
> Hello everybody,
> i want to convert my genotyping results (from CRLMM) to PLINK.
> For an case/control- study I genotyped 100 Affymetrix Human-Wide SNP Arrays 6.0. So I got my results like this (in extracts)
>
>
>               K_125.CEL K_128.CEL K_129.CEL K_134.CEL
> SNP_A-2131660         2         3         3         3
> SNP_A-1967418         3         3         3         3
> SNP_A-1969580         3         3         3         3
> SNP_A-4263484         2         2         3         3
>
>
> Genotype calls (1-AA; 2-AB; 3-BB)
>
>
>
>
> I want to use PLINK for my study and therefor I need an pedigree- file and an map- file. The ped- file is easy to create. It looks like 
> Patient01Patient010012
> Patient02Patient020021
>
>
> and so on....
>
>
> Is there any package or program, to convert my results for PLINK? Would be helpful, if there is anybody who can help me out. For this I need an map file and an peed- file. I read something about an "advanced" ped-file like this:
>
>
> Patient01Patient010012    A A  A C
> Patient02Patient020021    C C  ....
>
>
> Any ideas? 
> Thanks in advance
> All the best
> Peter
>
>
>
>
>
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