Statistical Tests for Genetic Associations (Permutation)

Question

[QVINTVS_FABIVS_MAXIMVS]

I'm doing a permutation (first time) and I see tests done like this figure below.

A distribution of simulated results are made. Then the observed value is plotted as a red line.

Then the authors usually report a Pvalue to the observed value.

How do I calculate this Pvalue?

Answer 1

[karl.stamm]

See the definition of a p-value.

In statistics, the p-value is a function of the observed sample results (a statistic) that is used for testing a statistical hypothesis. More specifically, the p-value is defined as the probability of obtaining a result equal to or "more extreme" than what was actually observed, assuming that the hypothesis under consideration is true.

, so just add up everything to the right of the red line. That's one tailed. Or do the absolute value so you get those x< -4 too. Be careful that your simulation matches the hypothesis. It's super important that your simulated data is made correctly.