search

cstubben / trinotateR

Trinotate annotation report summaries in R
12 stars 6 forks source link

Error for most trinotateR functions: Error in eval(bysub, x, parent.frame()) : object 'go' not found #2

Open browngcm opened 7 years ago

browngcm commented 7 years ago

Hello, I just generated a Trinotate annotation report, and I'm trying to summarize the findings of the report with trinotateR. I can run all of the functions outlined in README.md, but when I try to summarize other aspects of the report using summary_GO, summary blast, summary_pfam, etc, I encounter this error:

summary_GO(x) Error in eval(bysub, x, parent.frame()) : object 'go' not found

For each of the summary functions, do I need to go through the same steps as outlined in the README.md file for the pfam summary table?

cstubben commented 7 years ago

Yes, you need to split the annotations into separate rows and columns first and then summarize. This should work for GO columns and the default is gene_ontology_blast.

go <- split_go(x)
summary_GO(go)