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Description
For the pathway analysis, we plan to:
- Identify the kegg pathways in which a metabolite is involved.
- For each pathway, run TwoSampleMR for each component metabolite.
- For each pathway, determine the percent of metabolites that were significantly associated with the outcome variable.
- Generate a bargraph showing the top few pathways ranked by percent of metabolites significantly associated with outcome.
Problem: This ranking is qualitative and does not identify if the top ranked pathway has a higher percent of significantly associated metabolites than expected by chance.
Approaches:
- Calculate a null distribution using 100 to 1,000 pathways. This is not feasible to calculate dynamically. Instead, we could precompute the null distribution and use it for every tested pathway.
2....
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