Inferring KEGG pathway abundances for significant orthologs only.

[Ariel Balter]

With the http request tool I posted

https://github.com/ohsu-microbiome/kegg_http_tools

I can query a reasonable number of KOs. I haven't tested the limits.

Hypothetically, I could query the 3300 or so KOs picrust give me in `KO_metagenome_out/pred_metagenome_unstrat.tsv`, and create an up-to-date table with the same format as `picrust2/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv` mentioned in [the docs](https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#how-can-i-determine-kegg-pathway-abundances-from-the-predicted-ko-abundances).

Rather than creating that table for ALL of the inferred KOs, I could make a smaller table with only the ones I deem significantly differently abundant (represented) in my groups.

Is there any reason why this would be a bad approach? Do I really need the full table of KO to KEGG pathays?

Actually, I've tried a request with up to 500 KOs and not problem, but maybe I shouldn't push it.

[Gavin Douglas]

Hey again,

I haven’t tried inferring pathways with only a subset of KOs in the mapping file, but I would suspect this would make the data harder to interpret. The main reason I think this is because you could artificially call pathways present / absent simply due to excluding certain KOs.

I think it would be more direct for you to run some sort of enrichment test to determine which pathways are enriched for the significant KOs.

Best,

Gavin

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/9a00321b-1cdf-4aa6-b8c3-9b8051b5df8a%40googlegroups.com.

[Ariel Balter]

I guess, short of having access to full KEGG, I could do multiple requests to get all the pathways for my KOs and build the entire table.

I was able to have KEGG process a request of 1000 KOs. But beyond that I was getting timeout errors.