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remove quantile QTL code and other cleanup#471

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danielnachun merged 5 commits intomainfrom
remove-quantile-qtl
Apr 18, 2026
Merged

remove quantile QTL code and other cleanup#471
danielnachun merged 5 commits intomainfrom
remove-quantile-qtl

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@danielnachun
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This PR fixes is mostly just a massive cleanup:

  • removes all quantile QTL code which should now live in the qQTLR repository
  • removes the plotting and UDR code
  • replaces UDR in the mash wrapper with the standard mashr covariance functions
  • optimizes and cleans up code in various places where we now have enough test coverage to make those changes confidently

The only user-facing changes are the deletion of the quantile QTL functions.

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codecov Bot commented Apr 18, 2026

Codecov Report

❌ Patch coverage is 94.62151% with 27 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.80%. Comparing base (0517999) to head (8e75d87).
⚠️ Report is 1037 commits behind head on main.

Files with missing lines Patch % Lines
R/mash_wrapper.R 84.90% 16 Missing ⚠️
R/mr.R 94.50% 5 Missing ⚠️
R/colocboost_pipeline.R 94.11% 4 Missing ⚠️
R/twas.R 98.87% 1 Missing ⚠️
R/twas_weights.R 96.42% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #471       +/-   ##
===========================================
+ Coverage   27.48%   83.80%   +56.32%     
===========================================
  Files          32       35        +3     
  Lines        4377     6527     +2150     
===========================================
+ Hits         1203     5470     +4267     
+ Misses       3174     1057     -2117     

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@danielnachun danielnachun merged commit 9847b40 into main Apr 18, 2026
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@gaow gaow deleted the remove-quantile-qtl branch April 19, 2026 13:27
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