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huilisabrina / HEELS

Heritability Estimation with high Efficiency using LD and Summary Statistics
MIT License
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how to get the.npz file? #3

Open AndyYang0924 opened 5 months ago

AndyYang0924 commented 5 months ago

Hello, I would like to inquire how to obtain the .npz file corresponding to the instruction --ld_fp for East Asian populations. Looking forward to your response. Thank you!

KKristyXiang commented 4 months ago

I don't know if it helps but I found the .npz file for the data used in demo section in their Zenodo: https://zenodo.org/records/7618667

huilisabrina commented 4 months ago

Hi @AndyYang0924 ,

Thanks for your interest in using our software! We don't have the reference for the East Asian populations. Note that our method requires matching sample between the sumstats and the LD, so you might want to obtain the LD information for the GWAS sumstats you're using, or generating them yourself if you have access to the genotypic information for that sample.

Thanks @KKristyXiang for referencing the Zenodo link! We uploaded some data there for the demo example in the wiki tutorial. I actually have the banded + low-rank approximation for the chromosome-wide LD in the UKB ready, and I'm just looking to share those data with the public efficiently.

Hui