genomic inflation factor calculation
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Entering edit mode
4.3 years ago
lilingjoyo ▴ 40

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$PVAL,1,lower.tail=FALSE); lambda <- median(chisq) / qchisq(0.5,1)  GWAS inflation factor qq plot • 4.4k views ADD COMMENT 0 Entering edit mode Which one the correct one? lambda <- median(chisq) / qchisq(0.5,1) or lambda <- median(chisq) / qchisq(0.456,1)  ADD REPLY 0 Entering edit mode @always_learning I think you have gotten confused:  qchisq(0.5,1)  is (approx) 0.456. You want to use: chisq <- qchisq(gwas$PVAL, 1, lower.tail = F)
lambda <- median(chisq) / qchisq(0.5,1)


OP's question cannot be answered without looking at their QQ plot, but I don't see why lambda of 1.03 would be an unusual value to obtain.