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getian107 / PRScsx

Cross-population polygenic prediction
MIT License
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setting mcmc iterations reverts to default #16

Closed rmandla closed 2 years ago

rmandla commented 2 years ago

Hi Tian,

I want to run prs-csx with many MCMC iterations, but when I set the number with --n_iter, only the default 1,000 iterations * number of populations are run. Looking at the source code, it seems I am running into this issue because I am not changing the --n_burnin value, so --n_iter is set back to default. Is this intentional? And if so, would you be able to update the docs to indicate it and/or have prs-csx raise an error if one is set without the other?

Thanks!

getian107 commented 2 years ago

Hi- yes this is intentional because usually a longer MCMC chain is coupled with a larger number of burnin steps, and it doesn't make sense to set n_burnin > n_iter. I'll update the docs. Meanwhile if you set both values you should be able to run a chain with desired iterations.

rmandla commented 2 years ago

Thanks!