I'm currently conducting a transcriptomics study on Nicotiana benthamiana, and have reached a point where i would like to conduct a GO enrichment analysis using GOseq or topGO. Of course neither of these have N. benthamiana supported natively, so i would have to provide the GO mappings N. benthamiana genes myself. Other studies using the same sequence and annotations have used GOseq and topGO, but do not go into detail in their methods sections how they did this.
Of course i could simply feed a fasta of the DEGs into blast2go, but i don't actually have blast2go, and i feel like i'm missing something.
GOseq takes its gene to category associations as a named listed of vectors, where each vector is the terms associated with each gene, as such, a GAF file isn't neccessarily the end of the solution anyway.
I'd create this object from the annotation txt file.
This seems to work almost perfectly, the functions in brackets next to the GO terms in the functional annotations file are un-helpfully worded, so i will have to use a few lines of gsub to remove bits of leftover text,