Create a pipeline to export finemapping results with automated QC(WIP)#1187
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rl3328 wants to merge 15 commits intoStatFunGen:mainfrom
Open
Create a pipeline to export finemapping results with automated QC(WIP)#1187rl3328 wants to merge 15 commits intoStatFunGen:mainfrom
rl3328 wants to merge 15 commits intoStatFunGen:mainfrom
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rl3328
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I added the
auto_decisionstep to the export pipeline.I reordered parts of the code and added the conditional_effect column after the process_top_loci step. This change addresses the issue introduced by automated QC, where some blocks have top_loci but no credible sets (CS) across all methods or coverage levels.
I modified some documentations in mnm_postprocessing.ipynb.(container, pipeline name, etc.)
I added a column to indicate the finemap_model used in the final exported top loci table.
Fixed a typo when I exporting Aging finemapping results.
To do:
To output diagnostic table for ColocBoost iteration.
To integrate this updated pipeline into mnm_postprocessing.ipynb
I might fix auto_decision() function in pecotmr for susie_rss, since there's NA in z and p_value for the variants in diagnostics for PD, which is multi_ancestry. There might be missing variants in LD panel. Not sure if this is the reason. Will look into it further...