Interpreting the output of score test using GENESIS
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@lassanaasamarakoon-22071
Last seen 4.2 years ago

Hi all, I have output from an association test, using a Score test, from GENESIS software. My output has the following variables: Score Var Score.Stat Score.Val

According the GENESIS manual, I was expecting “Score.SE” and not “Var” variable. I want to confirm if the “Var” is Variance? If so, can I use √Var/√n to calculate the SE?

I really appreciate your help.

genesis output score • 1.3k views
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@stephanie-m-gogarten-5121
Last seen 17 hours ago
University of Washington

You must be using an old version of GENESIS, but looking at the manual for the current version. Var is indeed the variance, and Score.SE = sqrt(Var) (no factor of n).

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Thanks so much, Stephanie!

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Hi, Is there anyway to convert the Beta estimate to a z-score here (equivalent to Score.Stat)?

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I'm not entirely sure what you're asking here, since the Score test doesn't give a beta estimate. Is this what you're looking for? https://support.bioconductor.org/p/119621/

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Hi Stephanie, I'm so sorry for the confusion. I want to do the opposite of the above link you sent. 1)I want to convert the beta estimates to get a z score?

2) I want to know what is the z score variable of the assoc test output, is it "Score" or "Score.Stat"?

Thanks so much for your help.

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1) The score test does not return a beta estimate, but you can get a good approximation of beta by taking Score/Score.SE^2); or, in your case, by taking Score/Var

2) Score.Stat is the test statistic, which is what you are thinking of when you say "z score variable". The current version of GENESIS returns a Score.Stat that is approximately Normally distributed (i.e. a z score); however, since you are using an old version of GENESIS, I can't remember if it returns that, or the square of that, which would follow a chi-square distribution with 1 d.f. To double check, the "z score" test statistic can be calculated as Score/Score.SE (or in your case Score/sqrt(Var)).

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