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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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LDPred-2 error: N/A values for beta_grid in genomewide scenario #38

Closed fmadani closed 2 years ago

fmadani commented 2 years ago

Hi @privefl,

I faced an issue where the values of beta_grid are N/A. image

Here is the related command line: beta_grid <- snp_ldpred2_grid(corr, df_beta, grid.param, ncores = NCORES)

I put all the required codes in a text file attached. LDPred-genomewide-grid.txt

I tested these codes three times, but got the same values (N/A). Also, I got warning 'stack imbalance' messages like this:

image

Please review this issue and let me know what causes it.

Regards, Farshad

choishingwan commented 2 years ago

Hi @fmadani,

As mentioned, this repo is more for general PRS tutorial and are not specific to LDpred2. For LDpred2 supports, I suggest you to ask the questions in: https://github.com/privefl/bigsnpr/issues

Thanks

privefl commented 2 years ago

Please stop opening issues here. If you have questions about LDpred2, open them at https://github.com/privefl/bigsnpr/issues. Also, please have a look at the LDpred2 tutorial (https://privefl.github.io/bigsnpr/articles/LDpred2.html), where you'll find the answer to your question.

fmadani commented 2 years ago

OK. I will open in bigsnpr, but please note LDPred-2 is part of the tutorial as well, and I am literally practicing the tutorial. I am not practicing bigsnpr.