cosmetics

R/bio/cp_utils.R

@@ -77,6 +77,7 @@ cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
     #    PANTHER10_ontology <- read.delim("http://data.pantherdb.org/PANTHER10.0/ontology/Protein_Class_7.0")
     #    pantherResults <-     enricher(gene = geneIds, organism = cp_species, qvalueCutoff = q_cutoff, readable = TRUE, TERM2GENE = PANTHER10_ontology) %>% summary()
 
+    # keggResults <-          clusterProfiler::enrichKEGG(gene = geneIds, organism = cp_species, qvalueCutoff = q_cutoff, use_internal_data=T) %>% as.data.frame()
     keggResults <-          clusterProfiler::enrichKEGG(gene = geneIds, organism = cp_species, qvalueCutoff = q_cutoff) %>% as.data.frame()
     reactomeResults <-      ReactomePA::enrichPathway(gene = geneIds, organism = cp_species, qvalueCutoff = q_cutoff) %>% as.data.frame()
     goResultsCC <-          clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "CC") %>% as.data.frame()