Hi,
I plan to use some functions from metaboAnalyst, such as, pathway enrichment, but I want to check if their internal KEGG pathways database is different from my pathways list extracted using KEGGREST. In other words, I made a list of KEGG pathways with corresponding compounds from KEGGREST R package, which has ~270 pathways for 'hsa'. And I want to see how many KEGG pathways metaboAnalyst will be used to map during enrichment, and also what compounds in those pathways.
Can anyone tell me how to extract their KEGG pathway database from metaboAnalystR function or metaboAnalyst API?
Thank you in advance!
1 answer
And I want to see how many KEGG pathways metaboAnalyst will be used to map during enrichment, and also what compounds in those pathways.
It may be better to send an email to metaboAnalyst support and ask this question. Since KEGG requires a license for use any attempt to mass extract data from metaboAnalyst, may not be kindly looked upon by them.
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