Commit d96e886e authored by Holger Brandl's avatar Holger Brandl

improved enrichement report

parent e2865be6
......@@ -66,6 +66,7 @@ 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)$entrez_gene_id
# DEBUG geneIds <- glMapped %>% ungroup %>% filter(contrast==contrast[1])$entrez_gene_id
# geneIds=.$entrez_gene_id
if(length(geneIds)>1500){
......@@ -78,7 +79,7 @@ cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
# 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()
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()
......
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