
Post by Jorien on May 25, 2020 8:14:28 GMT
Hi! I have a question about the standardization step of GSMR as described at cnsgenomics.com/software/gsmr/. The instructions state that the input should be allele frequencies, zstatistics and sample size. Could you please clarify what is meant exactly with zstatistics here? I assume it is not standardized, zscores, as the script also requires you to include SEs. In my case, the unit of the effect size I have is an unstandardized beta (a volume measure), would it be correct if I input these unstandardized betas and use the standardization step to get to a standardized beta? Thank you in advance!


ax
New Member
Posts: 26

Post by ax on Jun 22, 2020 6:00:53 GMT
Hi Jorien, The standardizaiton step is only for beta and se estimate, while Zstatistic is already a standardized statistic. When you standardize the estimate, the actual process is 1. You input allele frequencies, zstatistics and sample size 2. Calculate the standardized se by se_new = 1 / sqrt(2*snp_freq*(1snp_freq)*(n+zscore^2)) 3. Calculate the standardized beta by beta_new= z / se_new So you could see that z didn't change after the standardization process. Hope this answer your question Cheers, Angli

