picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2

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Assign general function from KEGG pathway in pathways_out

Dirrrrty opened this issue · comments

I have the pathway output from PICRUST2 but the pathways are the specific pathway names such as 'COA-PWY' and 'ARGORNPROST-PWY' but I want to summarise them by their general functions like carbon metabolism, nitrogen metabolism etc. Currently I am searching each pathway in metacyc and biocyc and then looking for them in KEGG but surely there is a faster way to do this? I thought maybe there is a function in PICRUST2 or a package that works in conjunction with it to assign these general functions?
Any help please :)

I'm afraid that I'm not personally aware of any way to do this, unless you can find a mapping file somewhere on the metacyc/biocyc website. I imagine that some of the issue could be pathways used for multiple general functions. You could try posting in the Google group though - that will get more eyes on your question and maybe someone else has come up with a way to do this :)