**180**wrote:

Hello everyone! I am trying to make a Q-Q plot to visualise p-values obtained from different models afterr runing GWAS analysis. The key thing is that I want to reflect p-values from the different models in one chart. I tried qq function in qqman package however it takes only a vector of one model as an input, so as a result, I get the following picture:

And what I am trying to should look like this:

I don't understand the desired plot. The QQ plot use the mean and variance of the vector you inserted to plot it against a normal distribution, I don't see how you can compare different vectors with different means and variances. Having said that, you can use the returned values from qqnorm to plot multiple vectors in one figure.

8.4kFor normal distribution it is always possible to do standartization (Normal => Standard Normal), so this is not a big problem. QQ plot does not require the distribution to be normal - sample quantiles of, e.g., exponential distribution, may be plotted against theoretical quantiles (https://stat.ethz.ch/R-manual/R-devel/library/stats/html/qqnorm.html , there is an example of chisq at the bottom).

But I agree with your answer to the question.

1.8k