I'm using kegga to get KEGG enriched pathways from a list of differentially expressed genes. 

If I understand correctly, KEGG has a hierarchy/classification for the pathways. For example. In the first level we have Metabolism, inside this category, in the second level we have Carbohydrate metabolism and in the third level we have Glycolysis. 

Here is the classification from KEGG: https://www.genome.jp/kegg-bin/get_htext?br08901

I was wondering if there is a way to tell kegga that we want an specific level for the results.

Thank you.  

I think you misunderstand. The hierarchy you are talking about is simply a way to group the pathways into groups, for people who are browsing on KeGG's website. But kegga doesn't use say, Metabolism as a term, because that's not a pathway. The only pathways are the things at the third level, like Glycolysis.

What kegga does is to get all the genes that map to each of the pathways and then does a hypergeometric test for each pathway. This is different from the GO DAG, which does collect each set of child terms into the parent term, all the way up to e.g., Biological Process.