Irrelevant play

scripts/lpls/rpy_go.py

@@ -152,7 +152,18 @@ def parents_dag(go_terms, ontology=['BP']):
                 edge_dict[nn] = [head]
     return edge_dict
 
-def gene_GO_hypergeo_test(genelist, universe, ontology = ['BP']):
+def gene_GO_hypergeo_test(genelist,universe="entrezUniverse",ontology="BP",chip = "hgu133a",pval_cutoff=0.01,cond=False,test_direction="over"):
     
-    pvals = geneGoHyperGeoTest(entrezGeneIds, lib=None, ontology=ontology[0], universe=universe)
-    return pvals
+    #assert(scipy.alltrue([True for i in genelist if i in universe]))
+    universeGeneIds=universe
+    params = rpy.r.new("GOHyperGParams",
+                       geneIds=genelist,
+                       annotation="hgu133a",
+                       ontology=ontology,
+                       pvalueCutoff=pval_cutoff,
+                       conditional=cond,
+                       testDirection=test_direction
+                       )
+    result = rpy.r.summary(rpy.r.hyperGTest(params))
+    
+    return rpy.r.summary(result), params