Question: How to do a conditional analysis (using a tagging SNP) with dosage data in PLINK?
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gravatar for joseuribesalazar
3.1 years ago by
joseuribesalazar0 wrote:

Hi all,

I performed an association analysis with dosage data (.gen and .fam files) with PLINK 1.9 using imputated data and got back the association p-value for each SNP. Now, I want to do another association test with the same data, but using the SNP with the strongest association signal as a covariate (a conditional test).

The problem is that when i try to use the --condition option, a message appears saying "--dosage doesn't allow the conditional option".

Has anybody had the same problem? Any possible solutions or help are extremely welcome, since I'm breaking my head over here.

Thank you!


Type of data that I have:

SNP     Position     A1       A2    ProbA1A1_Subject1   ProbA1A2_Subject1   ProbA2A2_Subject1... for 5000 subjects
snp • 1.4k views
ADD COMMENTlink modified 7 months ago by RamRS21k • written 3.1 years ago by joseuribesalazar0

The dosage part of PLINK is under development, as far as I'm aware: https://www.cog-genomics.org/plink/1.9/order#dosage

Note that you can do what you want in R. I have processed whole genome genotyping PLINK data in R.

ADD REPLYlink written 7 months ago by Kevin Blighe41k
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