7.6 QQ plots

One common visualization for GWAS results is a QQ plot, which compares the distribution of p-values in our results to a null distribution (i.e., the uniform distribution that we plotted earlier).

How do you make a QQ plot?
  • Generate simulated p-values from a uniform distribution – the number of simulated p-values should equal the number of actual p-values
  • Sort both your real and simulated p-values in descending order
  • Plot the first, second, third, etc. p-values, where
    • x-axis is the simulated value
    • y-axis is the actual value
Fig. 5 (source). QQ plots visualize the distriution of p-values compared to a null distribution.
Fig. 5 (source). QQ plots visualize the distriution of p-values compared to a null distribution.

There are three areas of this plot where points can fall:

  1. On the \(\mathbf{x = y}\) line: No association signal
  2. Above the \(\mathbf{x = y}\) line: Some association signal
  3. Below the \(\mathbf{x = y}\) line: Issue with our statistical test (ex: not appropriately adjusting for covariates)
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