Entering edit mode

lassana.a.samarakoon
▴
10

@lassanaasamarakoon-22071
Last seen 2.7 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.

Thanks so much, Stephanie!

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

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/

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.

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)`

).