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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).
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #102 +/- ##
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- Coverage 81.32% 81.30% -0.03%
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Files 14 14
Lines 4322 4396 +74
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+ Hits 3515 3574 +59
- Misses 807 822 +15 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Solve some bugs:
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.