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jbloomlab / phydms

phylogenetic analyses informed by deep mutational scanning data
GNU General Public License v3.0
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Rel fdr #36

Open jon-mah opened 4 years ago

jon-mah commented 4 years ago

This PR implements a method for computing the false discovery rate for the random effects likelihood method for inferring sites under diversifying selection.

@skhilton: The purpose of this was to introduce the FDR control method. I computed the expected values by hand (actually by excel), to make sure that we are computing FDR correctly. When you get a chance, can you take a look at check over any of the things I might have missed?

skhilton commented 4 years ago

@jon-mah: When you get a chance can you look at the changes I made?

  1. I translated your code into pandas functions
  2. I added some writeup to the docs about the FDR.

Can you think of

  1. other places in the docs where we should talk about FDR?
  2. ways to make the current FDR text in the docs better?