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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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Add print-coefficient flag #20

Closed quattro closed 4 years ago

quattro commented 4 years ago

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 commented 4 years ago

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 notifications@github.com 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!

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davidaknowles commented 4 years ago

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

omerwe commented 4 years ago

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 notifications@github.com wrote:

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

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