Question about the QQ-plot

Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/

GNU General Public License v3.0

162 stars 25 forks source link

Question about the QQ-plot #116

Open Youpu-Chen opened 2 weeks ago

Youpu-Chen commented 2 weeks ago

Hi there. Thx for this amazing and convenient toolkit!

I've encountered a problem about QQ-plot.

When I conduct the GWAS analysis with the top20 PCs, but it still looks like it is affected by the population stratification.

However, the lambda is relatively low (0.94).

If you could give me a hint, I'll really appreciate it.

Best regards.

Cloufield commented 2 weeks ago

Hi, Youpu,

to calculate lambda GC, we use the chisq statistic when P=0.5. So it corresponds to -log10(0.5) = 0.3 If you check the dots around X=0.3. It indeed seems that it is a little deflated.