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New release on Aug 26, 2025#102

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gaow merged 21 commits intoStatFunGen:mainfrom
xueweic:main
Aug 27, 2025
Merged

New release on Aug 26, 2025#102
gaow merged 21 commits intoStatFunGen:mainfrom
xueweic:main

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@xueweic
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@xueweic xueweic commented Aug 25, 2025

  • Solve some bugs:

    • lower threshold for removing spurious for LD free and M=1 iteration versions (but no simulation evaluations)
    • missing values (NA or NaN) in LD matrix error (var_r is not a logic value)
    • fix error for get-cos-summary
    • handle error since the best joint update jk-star is not included in the specific dataset
    • mismatched focal outcome index when we have multiple sumstat and few LD matrix (added unit test)
    • fix error when variable names in different datasets have different orders (e.g., dataset1 has A then B, but dataset2 has B then A).
  • optimize LD free version where we did not need generate a huge identity LD matrix to save memory usage

  • adding labeling horizontal and vertical space in colocboost_plot function.

xueweic and others added 21 commits May 6, 2025 08:43
checking missing values in LD matrix:
- will cause an error with 'var_r' is not a logic value
remove the construction of the diag LD matrix to save the memory.
fix error for get_cos_summary
slient the warning message from qvalue function, and if warning happens, try another qvalue estimation of pi0
The issue: if we have multiple sumstat and only one superset LD matrix, the index of focal outcome will be mismatched.

1. dict is designed by X and LD, but we need additional dictionary for keep variables.
2. keep variables for individual level data is based on X - there is no issue.
3. keep variables for sumstat data is based on sumstat (not LD) - there is a issue to index the focal outcome based on dict later.

Keeping and commenting out the original code for initial testing, later we will remove the commented code if pass the test

Additionally:
1. adding unit test for the above issue.
2. debuging the data loader error.
Handle error since the best joint update jk_star is not included in the specific dataset. We will not consider LD for this update.
Adding uCoS filtering cirtieria
- check_null_max_ucos
adding horizontal and vertical spaces of text labels.
fix error when variable names in different datasets have different orders (e.g., dataset1 has A then B, but dataset2 has B then A).
@xueweic xueweic requested a review from gaow August 25, 2025 16:44
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codecov Bot commented Aug 25, 2025

Codecov Report

❌ Patch coverage is 75.73529% with 33 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.30%. Comparing base (8a97681) to head (aeb4d1c).
⚠️ Report is 31 commits behind head on main.

Files with missing lines Patch % Lines
R/colocboost_utils.R 25.00% 15 Missing ⚠️
R/colocboost_inference.R 58.33% 10 Missing ⚠️
R/colocboost_update.R 75.00% 3 Missing ⚠️
R/colocboost.R 71.42% 2 Missing ⚠️
R/colocboost_init.R 93.75% 2 Missing ⚠️
R/colocboost_check_update_jk.R 87.50% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #102      +/-   ##
==========================================
- Coverage   81.32%   81.30%   -0.03%     
==========================================
  Files          14       14              
  Lines        4322     4396      +74     
==========================================
+ Hits         3515     3574      +59     
- Misses        807      822      +15     

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@gaow gaow merged commit b6d7e37 into StatFunGen:main Aug 27, 2025
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2 participants