I'm using clusterProfiler for gene enrichment analysis and would like to check how enriched are specific GO terms.
For example, I have df with DEx genes (experimental vs control) and would like to see how GO:0043066 is enriched, not just which GO terms are enriched.
My approach is following:
- intersections between list of upregulated genes in experimental group and genes from GO term of interest
- setting universe in enrichGO function as all of my expressed genes
dnarepair.genes <- intersect(DEG$endo$genes, go_list$dnarepair) X <- enrichGO(dnarepair.genes, universe=allgenes, #(rownames(seurat)[Matrix::rowMeans(seurat$RNA@data !=0) >= 0.1]) ont = 'ALL', keyType = "SYMBOL", pvalueCutoff = 0.05, OrgDb = org.Mm.eg.db)
Any suggestions? Thanks!