Question: Calculate genomic inflation factor lambda for meta-analysis run in PLINK?
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gravatar for dam4l
2.3 years ago by
dam4l120
dam4l120 wrote:

I meta-analyzed the results of 2 genome-wide association studies using PLINK.

plink --meta-analysis file1 file2 + logscale qt --out results

I created a Q-Q plot with the resulting p-values. The p-values look to be inflated. I am unsure whether this is resulting from inadequate control for population substructure or if it is due to the polygenicity of the phenotype. I would like to know the value of the genomic inflation factor lambda (which was calculated using PLINK with the --adjust flag in the original GWAS - neither used in the meta-analysis were inflated).

Is there a way to have PLINK calculate the genomic inflation factor lambda and output it in the log file for a meta-analysis of multiple GWAS in the same that it can be done for a single GWAS?

Any input or suggestions would be appreciated.

snp plink gwas gwama • 1.5k views
ADD COMMENTlink written 2.3 years ago by dam4l120

Related post: Calculating Genomic Inflation Factor

ADD REPLYlink written 5 months ago by zx87546.8k
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