Converting Genotyping result for PLINK
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Peter Ganske ▴ 50
@peter-ganske-3745
Last seen 7.1 years ago
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 The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.
convert convert • 3.1k views
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@claus-jurgen-scholz-3117
Last seen 7.1 years ago
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 > > > > > > The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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