Error in running `GO_similarity`

[kanekalla]

Hi @jokergoo ,

Thank you for another wonderful package.

I am having issues running GO_similarity function. In the R notebook, when I run it for the first time it works and if I am rerunning the same code it gives me the following error.

mat = GO_similarity(gprofiler2_result$term_id,db = 'org.Mm.eg.db') Error in match.arg(ont, c("BP", "CC", "MF")) : 'arg' should be one of “BP”, “CC”, “MF”

Is there anything that I am doing wrong?

[kanekalla]

It worked when I mentioned ont= "BP", so should I give the argument by default?

[jokergoo]

I guess your GO list (gprofiler2_result$term_id) is a mixture of BP/CC/MF terms, so that the function can not automatically determine which ontology to use. If you are sure your GO list is from one unique ontology, then you can leave ont argument out, or else you need to specify ont.