I ran into a labelling problem with one package later on and would like to know if it is possible to manually change the rownames(res) for specific selected IDs without having to edit the initial counts df and run the analysis again.

[1] "OG_0"    "OG_1"    "OG_10"   "OG_100"  "OG_1000" "OG_1001" "OG_1002" "OG_1003" "OG_1004" "OG_1005" "OG_1006" "OG_1007" "OG_1008" "OG_1009" "OG_101"  "OG_1010"

where ie: OG_0 = "gene A" OG_234 = "gene B"

I tried this but it does not work

rownames(res$priorinfo$rownames)[rownames(res$priorinfo$rownames) == "OG_0"] <- "gene A"

You can add a new column to your results table that contains the new gene names, and then use that new column for EnhancedVolcano. Or, you can just create a new independent character vector and, instead, pass that to EnhancedVolcano.

Kevin