Question: Genomic Inflation Factor for GWAS of Quantitative Trait
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gravatar for brde4939
3.2 years ago by
brde49390
brde49390 wrote:

Hello,

I have performed a GWAS on a quantitative trait and would like to calculate the genomic inflation factor (lambda). Does anyone have advice on how to do that, or programs they would suggest?

I see that if I run the analysis in plink with the command below I do get an estimation of the genomic inflation factor in the log file, but I would also like to be able to calculate the genomic inflation factor on a separate set of p-values I have from an analysis not completed in plink.

plink --bfile data --pheno data.pheno --linear --adjust --out gwas.data

 

Thank you!

 

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ADD COMMENTlink modified 2.6 years ago by Tobias.Wohland60 • written 3.2 years ago by brde49390
0
gravatar for Tobias.Wohland
2.6 years ago by
Germany
Tobias.Wohland60 wrote:

Hi,

although you asked a couple of months ago, I hope my answer helps. This post should help you with the calculation. However, there are also programs available to do it directly. I personally use GenABEL, an R-package for GWAS. It has the function estlambda() to estimate lambda. You can either provide p-values or chi-squares with 1 d.f. Here is the actual link to the function and the package itself.

Best, Tobi

ADD COMMENTlink written 2.6 years ago by Tobias.Wohland60
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