genomic inflation factor calculation

Question

[lilingjoyo]

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)

[always_learning]

Which one the correct one?

lambda <- median(chisq) / qchisq(0.5,1) 
or
lambda <- median(chisq) / qchisq(0.456,1)

[anailis]

@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.