Question: genomic inflation factor calculation
gravatar for lilingjoyo
22 months ago by
lilingjoyo30 wrote:

hallo, everyone.

I'm new to GWAS data analysis. When I do QQ plot for my association analysis result produced by snptest software. The observed p-value is deviated from expected p-value. But the inflation factor lambda is quite small, it's only 1.03. How to explain this phenomenon. Followings are my codes.

chisq = qchisq(gwas$PVAL,1,lower.tail=FALSE);
lambda <- median(chisq) / qchisq(0.5,1)
inflation factor qq plot gwas • 1.7k views
ADD COMMENTlink written 22 months ago by lilingjoyo30
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