Z-score or effect and standard error
plbngl opened this issue · 6 comments
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
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))
Hi HaniceSun,
I have a similar question.
Did you try your method to get SE from RASQUAL? It works or not?
Thank you
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
HI Hanice,
Thank you for the reply. I will try.
Best,
Hongbo