Commit e3b6c852 authored by Holger Brandl's avatar Holger Brandl

keep gene ids in enrichment report

parent 12bcf853
......@@ -80,10 +80,10 @@ cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
# 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, keyType="ncbi-geneid", 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()
goResultsMF <- clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "MF") %>% as.data.frame()
goResultsBP <- clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "BP") %>% as.data.frame()
reactomeResults <- ReactomePA::enrichPathway(gene = geneIds, organism = cp_species, qvalueCutoff = q_cutoff, readable = TRUE) %>% as.data.frame()
goResultsCC <- clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "CC", readable = TRUE) %>% as.data.frame()
goResultsMF <- clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "MF", readable = TRUE) %>% as.data.frame()
goResultsBP <- clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "BP", readable = TRUE) %>% as.data.frame()
#cp-bug: if no pathways are enriched odd strucuture is retured ##todo file issue
if(!("data.frame" %in% class(keggResults))) keggResults <- filter(goResultsBP, Description="foobar")
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment