Z-score or effect and standard error

[plbngl]

Dear Natsuhiko,
thanks again for the great tool!
I was wondering if it is possible to obtain z-scores or effect size AND standard errors from rasqual outputs.
I would like to perform downstream analyses to compare QTLs across conditions and they require these values.
Thank you very much for your help,

Best,
Paola

[HaniceSun]

Dear Natsuhiko,

I have a similar question.
I would like to do colocalization analysis using coloc, which recommends using beta and SE (or var) of beta.
It seems beta is Effect size (Pi) - 0.5 in the RASQUAL output, but could you please advise me on how to get the SE value?
Thanks a lot.

---

Just saw discussions on this post and this paper.

It seems we can estimate both beta and SE of beta given z-score, allele frequency, and sample size.
SE =1 / sqrt(2p(1− p)(n + z^2))
beta = z * SE

So is it correct to get SE from RASQUAL output bellowing?
SE =1 / sqrt(2 * Allele frequency (1− Allele frequency )(n + Chi square statistic)), n is the sample size we know as an input.

---

It seems we can estimate SE here simply as bellowing:

SE = abs(beta/np.sqrt(Chi square statistic))

[hbliu]

Hi HaniceSun,
I have a similar question.
Did you try your method to get SE from RASQUAL? It works or not?

Thank you

[HaniceSun]

Hi Hongbo,

I believe it is correct. The results make sense when I use the SE this way in the cloloc analysis with both ABF and SuSiE method.

Hi HaniceSun, I have a similar question. Did you try your method to get SE from RASQUAL? It works or not?

Thank you

[hbliu]

HI Hanice,

Thank you for the reply. I will try.

Best,
Hongbo