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Question: Statistical Tests for Genetic Associations (Permutation)
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gravatar for QVINTVS_FABIVS_MAXIMVS
5.3 years ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
USA SoCal
QVINTVS_FABIVS_MAXIMVS • 2.4k wrote:

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?
statistics genetics test gene permutation • 2.1k views
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modified 5.3 years ago by karl.stamm ♦ 3.9k • written 5.3 years ago by QVINTVS_FABIVS_MAXIMVS • 2.4k
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gravatar for karl.stamm
5.3 years ago by
karl.stamm ♦ 3.9k
United States
karl.stamm ♦ 3.9k wrote:

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.
ADD COMMENT • link modified 14 months ago by _r_am ♦ 32k • written 5.3 years ago by karl.stamm ♦ 3.9k
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