Commit 9b213795 authored by Holger Brandl's avatar Holger Brandl

use remote kegg for enrichment (since local data is buggy and comes without IDs)

parent 4f57eeb8
......@@ -64,6 +64,7 @@ find_enr_terms = function(ensemblIds, ...){
cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
# DEBUG geneIds <- glMapped %>% filter(cluster %in% c("cluster_9")) %$% entrez_gene_id %>% as.integer
# DEBUG geneIds <- glMapped %>% filter(cluster_id %in% c("nr1")) %$% entrez_gene_id %>% as.integer
# DEBUG geneIds <- head(glMapped,30)$entrez_gene_id
# geneIds=.$entrez_gene_id
......@@ -76,7 +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()
goResultsMF <- clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = q_cutoff, ont = "MF") %>% as.data.frame()
......
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