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ajaynadig / bhr

Suite of heritability and genetic correlation estimation tools for exome-sequencing data
MIT License
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How to obtain 'n_eff' #13

Closed hoangthienan95 closed 1 year ago

hoangthienan95 commented 1 year ago

Hi there,

I'm trying to run my own BHR analysis using sum stats from genebass. However, I got stuck on this line: https://github.com/ajaynadig/bhr/blob/40b4a8a2f0315548910dd0fd3d7287f69432bbb6/example/genebass_variant_filter_january_2023.py#L25-L27

The Supplementary Table column key define n_eff as "Effective sample size from Genebass analysis for continuous traits" but I can't find where the n_eff column is in the Genebass data (gs://ukbb-exome-public/500k/results/variant_results.mt). Supplementary table 5 of the paper has n_eff for only 37 traits.

Where can I find n_eff? Thanks!

ajaynadig commented 1 year ago

Hello, Estimates of N_effective (computed with SAIGE) for all genebass traits can be found in this public HailTable:

gs://ukbb-exome-public/500k/qc/n_eff.ht

hoangthienan95 commented 1 year ago

Thanks for the rapid response!!!!

ajaynadig commented 1 year ago

No problem, feel free to reopen if you have additional issues