Remove get_hpo function

neurogenomics · Jan 8, 2025 · 87f2671 · 87f2671
1 parent 11553e7
commit 87f2671
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Showing 5 changed files with 21 additions and 89 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -22,7 +22,6 @@ export(get_gencc)
 export(get_gene_lengths)
 export(get_genes_disease)
 export(get_graph_colnames)
-export(get_hpo)
 export(get_monarch)
 export(get_monarch_files)
 export(get_monarch_kg)

diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,8 @@
 * `get_opentargets`: Limit threads and files to import in example.
 * Merge fixes by @HDash https://github.com/neurogenomics/KGExplorer/pull/2
 * `dt_to_kg`: fix reference to graph `g`.
+* `get_hpo`
+  - Remove ported function to avoid conflicting namespaces. Instead, simply use `get_ontology("hpo")`
 
 # KGExplorer 0.99.05
 

diff --git a/R/get_hpo.R b/R/get_hpo.R
diff --git a/R/map_upheno_data_i.R b/R/map_upheno_data_i.R
@@ -27,7 +27,7 @@ map_upheno_data_i <- function(pheno_map_method,
       pheno_map[,db1:=gsub("*:.*","",basename(id1))]
     } else if(pheno_map_method=="monarch"){
 
-      hpo <- get_hpo()
+      hpo <- get_ontology(name = "hpo")
       out <- monarchr::monarch_search(query = NULL,
                                       category = "biolink:PhenotypicFeature",
                                       limit = 500)

diff --git a/man/get_.Rd b/man/get_.Rd