paturley

Yeah, you might be right. MTAG requires being able to get a good estimate of the heritability and genetic correlations, which it can't easily do if there is very high...

I've not tested the robustness of MTAG with fewer than hundreds of thousands of SNPs, so I'm not sure what the threshold is before MTAG results are reliable. One thing...

Hi KJ, That is a great question. While at an individual SNP level, MTAG estimates should be unbiased and have standard errors with correct coverage (as long as MTAG's assumptions...

We never explored this very fully in the paper, so I don't have any careful analysis to point to justify this claim, but based on a handful of subsequent examples...

Hi Stefan, Apologies for the delay in replying. If a SNP is significant before applying MTAG but not afterwards, it is likely because the beta estimate for the correlated trait...

The mean chi2 scales with the sample size and heritability of the traits you use. With just 50k samples in your data, your mean chi2 stats seem about right to...

Yeah. You might consider calculating the maxFDR for each trait run separately as a baseline. The maxFDR will likely be pretty high then as well. On Tue, Jan 29, 2019,...

No problem. Glad to help. On Wed, Jan 30, 2019 at 8:11 AM mpx353 wrote: > Just for your interest: Since the maxFDR was quite high, I was interested >...

I don't know that there is a clear threshold. It really depends on the application. Have you run maxFDR on each of the sets of summary statistics separately? Sometimes that's...

MTAG will work fine if traits have a negative genetic correlation as long as the assumptions of MTAG are met. More precisely, I should have said that SNPs may fall...