Statistical Tests for Genetic Associations (Permutation)
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6.6 years ago

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?

permutation genetics gene test statistics • 2.5k views
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Entering edit mode
6.6 years ago

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.

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