paturley

It depends on what you are trying to do. MTAG is meant to produce summary statistics that correspond to each of the input phenotypes. However, from this summary table, I'm...

This is explained in the MTAG paper. The formula for it is N_GWAS*(1-meanChi2_MTAG)/(1-meanChi2_GWAS). It's meant to approximate how large a sample you'd need to produce a GWAS that equally powered...

Which question? Sorry, I'm not sure what you are referring to. On Tue, Nov 7, 2023 at 11:04 AM caozilongsupper ***@***.***> wrote: > Thanks for your explanation and I got...

No worries. As I mentioned above, MTAG produces one set of summary statistics for each trait. So the difference in the effect size estimates is because the estimated effect of...

Hi Suzy, MaxFDR gives the potential maximum FDR for MTAG results. So a maxFDR means that up to 5% of the SNPs that are genome-wide significant may be false positives....

A couple years ago, we noticed a few anomalies in MTAG results when the beta/se option was used that made us worry that the results weren't reliable. So we removed...

I mentioned this in #185 as well. If you pass a single trait through MTAG, the beta values that are output should be a constant multiple of the input betas....

Hmm. This is a bit of a puzzle to me to. The main thing I find strange is that the mean chi2 for trait1 falls after MTAG. Because MTAG SEs...

The current MTAG software can only handle SNVs, though as you saw in another issue, it sounds like it's not too complicated to edit your local instance of MTAG to...

I suspect that the problem is because LDSC doesn't allow for non-SNVs and may require rsids (which would be a problem with the reference data, as you said), and MTAG...