Importing eggnog annotations into topGO or similar?
Entering edit mode
2.4 years ago
rmash ▴ 20

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
RNA-Seq EGGNOG GO terms non-model organism • 1.4k views
Entering edit mode

Without seeing the file content, one can only guess at what the problem is although most likely it is a data format issue. Check that your file conforms to what's expected by the readMappings function, i.e. columns are tab-separated and the first one contains gene IDs, the second one a comma-separated list of GO term IDs, e.g.:

068724  GO:0005488, GO:0003774, GO:0001539, GO:0006935, GO:0009288
119608  GO:0005634, GO:0030528, GO:0006355, GO:0045449, GO:0003677, GO:0007275
Entering edit mode

Thanks, you were right!

This is more of an issue with EggNOG but do you find that it doesn't assign GO terms to most of the orthologs?


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