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Pathway analysis workflow

Pathway analysis for MR BACOn.

1. Map metabolites with their HMDB (and KEGG) ids using the Chemical Translation Service.

Provided by the West Coast Metabolomics Center.

2. Obtain the complete metabolite xml file from the Human Metabolome Database.

3. Parse xml file, get pathway information.

 ./parse_pathways.pl xmlfile.xml

4. Get a list of metabolites that are in the same pathways as the user-defined metabolite-of-interest.

 get_metabolites_from_pathway.R

5. Run TwoSampleMR for each metabolite returned from step 4.

How to run TwoSampleMR

6. Calcualte average association score for each pathway, get top ranked pathways.