Commit 103e1e55 authored by Holger Brandl's avatar Holger Brandl

cosmetics

parent 211934b5
......@@ -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()
......
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