positive-containing DFE from Zhen et al 2021 (GammaPos_Z21, HomSap and DroMel) #1656
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## main #1656 +/- ##
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Coverage 99.84% 99.84%
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Files 132 132
Lines 4584 4616 +32
Branches 467 467
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petrelharp
changed the title
petrelharp
commented
Jan 22, 2025
| @@ -36,20 +36,83 @@ def _HuberDFE(): | |||
| distribution_type="g", # gamma distribution | |||
| distribution_args=[gamma_mean, gamma_shape], | |||
| ) | |||
| # p. 2 in supplement says that the total sequence length of synonymous sites LS | |||
| # related to the total sequence length LNS by LNS = 2.85 * LS; | |||
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| # related to the total sequence length LNS by LNS = 2.85 * LS; | |
| # related to the total sequence length of nonsynonymous sites LNS by LNS = 2.85 * LS; |
petrelharp
commented
Jan 22, 2025
| distribution_args=[gamma_mean, gamma_shape], | ||
| ) | ||
| # p. 2 in supplement says that the total sequence length of synonymous sites LS | ||
| # related to the total sequence length LNS by LNS = 2.85 * LS |
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Suggested change
| # related to the total sequence length LNS by LNS = 2.85 * LS | |
| # related to the total sequence length of nonsynonymous sites LNS by LNS = 2.85 * LS |
petrelharp
commented
Jan 22, 2025
| distribution_args=[gamma_mean, gamma_shape], | ||
| ) | ||
| # p. 2 in supplement says that the total sequence length of synonymous sites LS | ||
| # related to the total sequence length LNS by LNS = 2.31 * LS |
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Suggested change
| # related to the total sequence length LNS by LNS = 2.31 * LS | |
| # related to the total sequence length of nonsynonymous sites LNS by LNS = 2.31 * LS |
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This is as recommended by @klohmueller over in #1469. It's really just Huber et al's Gamma_H17 except a proportion
pof the changes are beneficial with coefficients; the paper shows thatpandsare highly confounded (andpscan be estimated better); but these are the MLE values. These values are using divergence to chimp.Kirk said:
What I've implemented is this, and I've verified all those parameters above - so, I figure this is actually mostly QC'ed (since Kirk pulled out those numbers and I verified them). So, I'm tempted to just put in the QC code also - but that wouldn't catch coding errors.
Edit: I've also added the estimated one for DroMelfrom Table S6 as above.