error in both R and command line

[Jie Huang]

Hi!

Please see the above screenshot, I got an error from R .

Please see the above screenshot, I also got an error from command line version.

Can you please let me know what I did wrong here?

Thanks!

Jie

[Lan Ao]

Hi,

Thanks for your feedback!
Could you please show me the content of the LD reference folder? (ls D:/data/ldsc/UKB_imputed_SVD_eigen99_extraction)

[Jie Huang]

yes, sure. please see below. I downloaded the file from the BAIDU link.

Best regards,
Jie

[Lan Ao]

There are duplicated files in the folder, you may delete them and try it again.
Please make sure that files within the folder are identical to what's in the network disk.

[Jie Huang]

Thank you very much! Now it works, after I removed the two files ending with "(1).Rdata" !
I assume these two files were generated when my downloading was interrupted and then got reconnected again. I assume that your HDL R script first calculates the number of files in the reference directory and then output an error if the file count is incorrect. Don't know if it is a good idea to modify your script a little bit so that it allows extra dummy files.

Please see the screenshot below. Even though now HDL runs, it could NOT calculate the genetic correlation between my two GWAS, because the first GWAS has a heritability of 0! The first GWAS is
a COVID-19 GWAS published last year on NEJM, so it is a very important GWAS, and that is why I try to dig into this.

BTW, I am a faculty at PKU https://sph.pku.edu.cn/info/1409/4174.htm
Don't know if Dr. Shen could still be reached at [e-mail].

[Lan Ao]

Too many SNPs in the reference panel are missed. You may estimate rg with LDSC or rebuild a LD reference panel for SNPs that appeared in both GWAS summaries.

Sorry, I'm not sure he's still using this e-mail or not. Anyway, you can try.