Several updates on Nov 6th #116
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Using profvis to check the computational time for each part of functions. Improve on several way: 1. check_pair_jkeach: instead of checking every pair, we check the upper tri first to reduce the burden. 2. Still some LD checking issue caused the LD-free mode. 3. change matrix multiplication using tcrossprod function
The highlighting feature has been updated to provide greater flexibility in visualization options. In previous versions, additional highlight variables in the colocboost plot could only be displayed as vertical lines by setting add_vertical = TRUE. The updated colocboost_plot function now offers more versatile highlighting capabilities through the new add_highlight = TRUE parameter, which allows users to display highlight variables as either vertical lines or red star markers, providing improved customization for data visualization needs.
To enhance computational efficiency, we pre-calculate LD values for each pair of outcome-specific best parameter updates at each boost update.
For the merged CoS, we recalibrate the CoS variants based on the merged weight. We should recalculate purity for the merged CoS and filter unpured merged CoS.
fix bug for choosing top variable in ucos details
fix fine-mapping one iteration issue
Comment out to avoid running this code here, as we do not have real data files in examples
handle duplication variables - remove one of them
1. Move colocboost wrapper to pecotmr. 2. Improve colocboost function - validation of the dataset. 3. Fix one error about the missing value or duplicated value in summary statistics
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Major change: Updated highlighting parameters in
colocboost_plotfunctionThe
colocboost_plotfunction now provides flexible highlighting options with the following parameter changes:add_vertical = TRUEtoadd_highlight = TRUE.add_vertical_idxtoadd_highlight_idx.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. We move the entire vignettes with the enhanced documentation to pecotmr.
Computational Improvements
Using
profvisto 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.tcrossprodfunction.Bug Fixes
purityfor merged CoS and filtered merged CoS whenpurity < min_abs_corr.