reverted back to clusterProfiler::bitr

common/cp_enrichment.R

@@ -128,11 +128,9 @@ annoDb <- guess_anno_db(geneLists$ensembl_gene_id) # e.g. "org.Hs.eg.db"
 
 ## convert to entrez gene ids
 
-#glMappedRaw <-  clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
-#    set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
+glMappedRaw <-  clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
+    set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
 
-glMappedRaw <-  bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
-  set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
 
 
 #' Check how many failed to map