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Merge pull request #4 from aaronkw/deepsea-scores
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Fix e-value formatting
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aaronkw committed Jan 30, 2020
2 parents ba57c25 + 71b11d6 commit 232b7c5
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4 changes: 2 additions & 2 deletions docs/deepsea.rst
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Expand Up @@ -72,12 +72,12 @@ Variant scores
* **Disease Impact Score (DIS)**: DIS is calculated by training a logistic regression model that prioritizes likely disease-associated mutations on the basis of the predicted transcriptional or post-transcriptional regulatory effects of these mutations (See Zhou et. al, 2019). The predicted DIS probabilities are then converted into 'DIS e-values', computed based on the empirical distributions of predicted effects for gnomAD variants. The final DIS score is:

.. math::
-log10(DIS e-value_{feature})
-log10(DIS evalue_{feature})
* **Mean -log e-value (MLE)**: For each predicted regulatory feature effect (:math:`abs(p_{alt}-p_{ref}`)) of a variant, we calculate a 'feature e-value' based on the empirical distribution of that feature's effects among gnomAD variants (see above Regulatory feature scores: e-value). The MLE score of a variant is

.. math::
\sum -log10(e-value_{feature}) / N
\sum -log10(evalue_{feature}) / N
In-silico mutagenesis
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