I am using goana to get enriched GO terms from my data. The problem I encounter is that I wish to find out what genes goana classes as 'up' or 'down' as the output from topGO() does not include this column.
I found a post from a number of years ago explaining how to do this with with the kegga() function and this works however I cannot find a way to alter the code for topGO(). I have included the code below from goana and topGO.
go <- goana(fit, geneid = fit$genes$ENTREZID, FDR=0.05, trend = F) DE_GOana <- topGO(go, ontology=c("BP"), sort = "down", number=Inf, truncate.term=50)