Hey Jordan (and all),
The question is not straight reply to this previous discussion but I have a question regarding the Qiime2r and phyloseq so I’ll just post it here.
I managed to import data from qiime2 to R and pyloseq without any major problems (if the lack of my experience is not considered as problem ).
I managed to work with different statistical tests and taxonomic-bar plots but I still have the taxonomic prefixes (k_ , p _ , etc) before my taxonomic names.
In phyloseq there is a command to parse these out if you are using qiime txt files and not qza files. If I understood correctly, this command is used in the importing phase using phyloseq (parseFunction=parse_taxonomy_greengenes).
Simple question, how to get rid off the prefixes?
As I said, I’m not so comfortable with R yet so there is probably a simple explanation how this can be done. Please correct me if I’m mixing things up!