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


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


Thank you!


open • 2.3k views
ADD COMMENTlink modified 2.6 years ago by Tobias.Wohland60 • written 3.2 years ago by brde49390
gravatar for Tobias.Wohland
2.6 years ago by
Tobias.Wohland60 wrote:


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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1017 users visited in the last hour