Commit f7cd9b7c authored by Holger Brandl's avatar Holger Brandl
Browse files

fixed enricher wrapper

parent b7e8f80e
......@@ -4,7 +4,7 @@
enrichr = function(geneSymbols, listName=NULL, ontologies=c("GO_Biological_Process_2015", "ENCODE_TF_ChIP", "ENCODE_Histone_Modifications_2015"), suppress_logs=T, keep_genes=F, padj_cutoff=0.05){
enrichr = function(geneSymbols, listName=NULL, ontologies=c("GO_Biological_Process_2015", "ENCODE_TF_ChIP-seq_2015", "ENCODE_Histone_Modifications_2015"), suppress_logs=T, keep_genes=F, padj_cutoff=0.05){
## todo remove listName from API
listHash=digest(geneSymbols)
......@@ -23,7 +23,7 @@ enrichr = function(geneSymbols, listName=NULL, ontologies=c("GO_Biological_Proce
# quote({
enrReusults = ontologies %>% map_df(function(ontology){
# ontology = "ENCODE_TF_ChIP"
# ontology = "ENCODE_TF_ChIP-seq_2015"
# enrichr-api/query_enrichr_py3.py ${geneList} "wgcna module ${geneList}" ENCODE_Histone_Modifications_2015 ${geneList}.encode_hist_meth_2015.enrresults.txt
resultsFile = tempfile(fileext=".txt")
......@@ -31,7 +31,7 @@ enrichr = function(geneSymbols, listName=NULL, ontologies=c("GO_Biological_Proce
if(file.exists(resultsFile)){
read_tsv(resultsFile) %>%
set_names("term", "overlap", "p_value", "adj_p_value", "z_score", "combined_score", "genes") %>%
set_names("term", "overlap", "p_value", "adj_p_value", "old_p_value", "old_adj_p_value", "z_score", "combined_score", "genes") %>%
mutate(
# list_name=listName,
ontology=ontology
......
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