I'm working with a non-model organism. I took some genes of interest and mapped it to eggnog. I got an annotation file that has a column with sometimes multiple GO terms per row.
What is the best way to look at GO term enrichment?
I can import the relevant columns (ID) and column with GO terms into R.
But do I still need a reference database now that these are mapped?
What's the best way to look like GO term enrichment?
This is what happens when I try to import my custom annation into topGO, where one column are some IDs and the second column is of GOterms
geneID2GO <- readMappings(file = "fc_test.csv", sep="\t") Error in `[.data.frame`(a, , 2) : undefined columns selected