KEGG database

[alicegrih]

Hi jtamames,

I used Squeezemeta to work with metatranscriptomic data and I followed the tutorial for data visualisation in Rstudio and I would like to ask 2 questions:

The first is that with the exportTable() function, I was able to download a database of KOs coming from the KEGG database, I would like to know if that table that I was able to download are only the KOs that were found in my samples or it is a direct database from KEGG and contains all the KOs registered in it.

And the second one is if you have any code where I can get all the KOs associated to a specific metabolic pathway, because I would like to know if I can perform an ORA and a GSEA, with the data I have.

Thank you, Best regards.

[fpusan]

Hi,

1) Hard to answer without knowing what what code did you exactly use. Probably all the KOs found in your samples.

2) See the code below

SQM.pwy = subsetFun(SQM, my_metabolic_pathway, columns="KEGGPATH") # create a subset containing only ORFs affiliated to the requested pathway
# `my_metabolic_pathway` can be a substring (no need to have the full pathway name though it will ofc be more specific
# `my_metabolic_pathway` can also be a regexp for more elaborate search patterns

rownames(SQM.pwy$functions$KEGG$abund) # All the KOs from the pathway

# Alternatively
exportPathway(SQM, pathway_id) # to export directly the KEGG map colouring the present reactions
# see the documentation for `subsetFun` and `exportPathway` for more usage details

[alicegrih]

Hi,

I appreciate your help.

Best regrets.

[fpusan]

Best regrets.

Ominous! Closing the issue, let me know if you need further help :)