paturley

Hello Crane, A key assumption of MTAG is that SNPs are exchangeable with respect to the correlation of effects sizes across traits. In practice, this is roughly equivalent to saying...

Hello Crane, I would just use the MAF from a reference panel. Assuming you choose a panel with approximately the same ancestry, the allele frequencies should be the same. On...

MTAG can account for negatively genetically correlated phenotypes. You shouldn't need to edit your summary statistics at all (beyond the usual QC). In the original MTAG paper, for example, we...

Hello Sander, The LD scores used by MTAG are the same as those used by LD Score Regression. So you should be able to use any LD scores that are...

Hello Zhou, I'm a bit confused about your comment. Are you using chicken summary statistics but a human LD reference panel? Patrick On Mon, Jan 18, 2021 at 9:49 PM...

Do you have a chicken reference panel? If so, you should be able to follow the directions at the LDSC wiki to generate new LD scores. https://github.com/bulik/ldsc/wiki/LD-Score-Estimation-Tutorial Once you have...

Hello! 1) They should be closely related. Genetic covariance is generally defined as either the covariance between the genetic components for a pair of traits or as the covariance of...

Hello, 1) I think that should work fine. Ideally, you would use the betas and standard errors directly from the logistic regression, but using log(OR) should give you approximately the...

Hello, Apologies for the slow responses here. I've been swamped by other projects so I haven't had time to dig deeply into your particular case. The genetic correlation matrix and...

Hi Stephen, Sorry about the delay here. This fell off my radar. I think part of the problem may be the units of the genotype. Since you are using beta=Z/sqrt(N)...