Genomic Inflation Factor for GWAS of Quantitative Trait

Question

[brde4939]

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!

Answer 1

[Tobias.Wohland]

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