This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Additive and dominance components for .ped file

I have list of SNPs and I'm trying to extract values for list of SNPs using below plink command:

plink --bfile Obesity_Send --extract MaleSNPsList.txt --recode --out MaleSNPsValues --noweb

which results .ped file, using --recodeAD I would like get Additive and dominance components for .ped file . For example, consider the following PED file, which has two SNPs:

 1 1 0 0 1  1  1 1  G G
 1 2 0 0 2  1  0 0  A G
 1 3 0 0 1  1  1 1  A G
 1 4 0 0 2  1  2 1  A A

Using the --recodeAD option generates the file plink-recode.raw:

     FID IID PAT MAT SEX PHENOTYPE snp1_2 snp1_HET snp2_G snp2_HET
 1 1 0 0 1 1  0  0   2 0
 1 2 0 0 2 1  NA NA  1 1
 1 3 0 0 1 1  0  0   1 1
 1 4 0 0 2 1  1  1   0 0

Desired Output:

     FID IID PAT MAT SEX PHENOTYPE snp1_2 snp1_HET snp2_G snp2_HET
 1 1 0 0 1 1  0  0   G G
 1 2 0 0 2 1  NA NA  A G
 1 3 0 0 1 1  0  0   A G
 1 4 0 0 2 1  1  1   A A

Any Suggestions & best methods much appreciated. I'm new to Plink please help

plink
• 1,024 views • link
updated by chrchang523 chrchang523 • written by Raju • Raju

1 answer

That .ped file is basically nonsense. You need to decide on a consistent method of encoding your alleles (probably replacing the “1”/“2” allele codes in your first variant with something more descriptive) before we can usefully talk about conversion to other formats.

• 0 views • link
written by chrchang523 chrchang523

Log in to answer this question.

More posts like this