How I can convert genotype data in a variety of pedigree formats R
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4.4 years ago
BlackHole • 0

I have a genotype data as a matrix of 10 samples (columns) and 560 000 SNPs (raws). I want to convert this data for further analysis , but have not MAP and PED file (PLINK format) to use GenABEL and I don't know any ways to do this conversion.

Here's a few rows and columns to show you what it looks like:

            S1  S2  S3  S4  S5
rs75406208  CC  CC  CG  CG  NA
rs200142685 AG  AG  GG  GG  GG
rs369829527 NA  NA  GG  GG  GG
rs76412254  GG  GG  GG  GG  GG
rs80033621  AA  AA  AA  AA  AA
rs62608737  GG  GG  GG  GG  GG
rs373506129 NA  NA  CC  CC  CC


Does anyone know any way to do it?

SNP R • 1.4k views
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Perhaps I missed something, but what's the D?

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D is deletion I is inversion And I have many polymorphisms such as AG, AT, AA , GG, CC, CG, TT

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I is insertion and not inversion that is something else

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of course, i confused

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This is weird. So you have a deletion for snp rs144430729, while that's a C/T SNP. Doesn't make sense to me. How did you obtain this data?

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It is not my data, I got them from my colleagues, to conduct a joint analysis with the metabolome

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If this is sequencing data, try to get the original output. That will make things less painful and less error-prone.

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4.4 years ago
Floris Brenk ▴ 980

Creating the ped file is easy with the information you already have. see for the format here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml just transpose what you have now and add a few columns:

 Family ID
Individual ID
Paternal ID
Maternal ID
Sex (1=male; 2=female; other=unknown)
Phenotype


For the map file you have to be a bit more creative and get the actual chromosome location etc of the snps probably by extracting it from dbsnp or similar.

 CHR RS-number score BP
1  rs123456  0  1234555

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I try to upload my data in dbsnp, but the end result was a blank sheet, and I got message that RS number(s) not found in dbSNP