Add print-coefficient flag

[quattro]

Hey Omer,

Awesome tool. Really enjoying it so far in our simulations. It would be great to include a flag to output the penalized taus, similar to the --print-coefficient flag in LDSC.

Thanks!

[omerwe]

Hi Nick, it's very easy to implement this, but I lean towards not doing it because the taus can be misleading. baseline-LF includes strongly correlated annotations, so it often happens that one annotation has a strongly positive and another annotation has a strongly negative tau, completely arbitrarily. I think the best way to estimate annotation importance this is to estimate h2 enrichment with S-LDSC, which is included in the Polyfun code (please see the FAQ). Other options would be to implement more modern feature-ranking methods (e.g. SHAP scores), which should be pretty simple. Happy to discuss more offline if you want to try to convince me otherwise :)

…

On Fri, Feb 14, 2020 at 5:36 PM Nicholas Mancuso ***@***.***> wrote: Hey Omer, Awesome tool. Really enjoying it so far in our simulations. It would be great to include a flag to output the penalized taus, similar to the --print-coefficient flag in LDSC. Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#20?email_source=notifications&email_token=ACNCB44PFAHUOYAAMEJKXNDRC4MGJA5CNFSM4KVRALWKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4INWHBSA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNCB46FUXOFSPY3AOK3N2DRC4MGJANCNFSM4KVRALWA> .

[davidaknowles]

Will this version of S-LDSC accept the same input files as polyfun?

[omerwe]

Yes, it should (PolyFun uses this version of S-LDSC internally). Please let me know if there's a problem!

…

On Tue, Feb 18, 2020 at 10:28 PM David A Knowles ***@***.***> wrote: Will this version of S-LDSC accept the same input files as polyfun? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#20?email_source=notifications&email_token=ACNCB42JQ33NO5NMYMFPQHDRDSRMNA5CNFSM4KVRALWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMGG3AQ#issuecomment-588017026>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNCB46S6MAI243ZOFJCILLRDSRMNANCNFSM4KVRALWA> .