Microbiome Stat for KEGG pathways

[OMIC-G]

Hi, thanks for such an useful tool! I am building a MicrobiomeStat from Matrix and Data.frame for KEGGS. The level separation (L1; L2; L3) works in the case of KEGGS with only one function, but ...
How could I create the feature.ann matrix in the case of KEGGs with more than one classification? An example would be KEGG K05881 "Metabolism; Lipid metabolism; Glycerolipid metabolism | Brite Hierarchies; Protein families: signaling and cellular processes; Transporters"

[cafferychen777]

Hello @OMIC-G,

Thank you for your interest in MicrobiomeStat and for your kind words! I appreciate your question about handling KEGG pathways with multiple annotations.

To better assist you, it would be helpful if you could provide a sample of your data. This will allow me to create a more accurate and tailored example for your specific use case.

If you're comfortable sharing, please send a small subset of your data that includes:

1. Your KEGG pathway matrix
2. The corresponding metadata
3. An example of how your current feature annotations look

Once I have this information, I can write a demonstration code that shows how to properly structure the feature.ann matrix for KEGG pathways with multiple annotations in MicrobiomeStat.

If you prefer not to share your data publicly, feel free to send it to me privately, and I'll ensure to remove any sensitive information when posting the solution.

Looking forward to helping you implement this in MicrobiomeStat!

Best regards,
Caffery