Jean Morrison

Yes. I used the supplementary material of [https://pubmed.ncbi.nlm.nih.gov/26414676/](https://pubmed.ncbi.nlm.nih.gov/26414676/) specifically the sections "Cross-trait LD score regression" and "Regression Weights" I also referenced the ldsc python code. Most relevant is [lines 538-711...

@privefl If you let me know what needs to be done I can see if we will have time to do it in the course of our work.

All makes sense. It currently produces SEs for the intercept and the genetic covariance but not genetic correlation which requires implementation of the ratio jacknife. I'll add some tests when...

This error means that there are variants in your `top_vars` list that are not in `X`. I don's see in your code where `top_vars` came from but hopefully that helps.

Try ``` all(top_vars %in% X$snp) ``` If that gives FALSE you have found the problem. Otherwise let me know.

Hello! I have occasionally seen warnings for the Pareto k diagnostic values but it is suspicious to me that 84% are in the very bad category. It seems like something...

I would be surprised if that was the explanation -- at least I have not seen this when I did tests with simulated low power GWAS. How many variants did...

I usually recommend to use a genome-wide set of LD-pruned SNPs for parameter estimation and down to a p-value of 1e-3 for model fitting. The model fit should not be...

I think this case is a little borderline personally. I think it is ok to make inference based on the 95\% credible interval for gamma, though in the paper we...

Thanks - that's great! I was also wondering a few more things 1. Is there a way to interpret Wellington bootstrap scores in terms of p-values or false discovery rates?...