Changing logs

[xueweic]

Major change: Updated highlighting parameters in colocboost_plot function

The colocboost_plot function now provides flexible highlighting options with the following parameter changes:

• change add_vertical = TRUE to add_highlight = TRUE.
• change add_vertical_idx to add_highlight_idx.
• add one additional add_highlight_style = "star", displaying highlights as red star markers.

For detailed examples, see the Visualization of ColocBoost Results. This update reflects user feedback and suggestions. We thank all users for their valuable suggestions that improved this functionality.

Minor changes:

• Thanks efforts from @kal26 to enhance the documentation and test examples for our wrapper pipeline. Commented out code examples to prevent execution during website build due to missing data files

• Computational Improvements
  Using profvis to check the computational time for each part of function components.

  • check_pair_jkeach: reduced computational burden by checking the upper triangle first instead of all pairs.
  • Addressed LD checking issues in LD-free mode.
  • Improved matrix multiplication efficiency using tcrossprod function.
  • Pre-calculated LD values for outcome-specific parameter updates at each boost iteration

• Bug Fixes

  • Recalculate purity for merged CoS and filtered merged CoS whenpurity < min_abs_corr.
  • Fixed error when focal outcome fails multiple testing correction at the first iteration in disease-prioritization mode
  • Fixed bug in top variable selection within uCoS details
  • Fixed one-iteration model for single-trait fine-mapping
  • Fixed variables duplication issues: only keep one if duplicated variables