Question: case control association analysis with covariates in plink?
gravatar for Sheila
3.7 years ago by
United States
Sheila330 wrote:


I would like to complete a case/control analysis with two covariates (sex and age) in plink. Here is my model

Y = B0 + B1X1 + B2X2 + B3X3

where... Y = Disease Status (0 or 1), X1 = given SNP, X2 = Sex, X3 = Age

I have a few questions:

This was my command:

plink --bfile myfile --assoc --covar --covarList.cov --out results

I realized i couldn't include covariates in a case control analysis in plink. That being said, would the --linear command provide me what I need (See command below)???

plink --bfile myfile --linear --covar --covarList.cov --out results

Would I need to create a pheno file if I use the --linear command or would the command above give me the results.

I basically am asking what is the correct command to achieve the results of my given model above.

Thank you!

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Sheila330
gravatar for chrchang523
3.7 years ago by
United States
chrchang5237.5k wrote:

--logistic is the command you're looking for.

ADD COMMENTlink written 3.7 years ago by chrchang5237.5k
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