feat(coloc effect sizes): update schema and coloc code

opentargets · Sep 30, 2024 · bee8bb9 · bee8bb9
1 parent 09c8580
commit bee8bb9
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diff --git a/src/gentropy/assets/schemas/colocalisation.json b/src/gentropy/assets/schemas/colocalisation.json
@@ -72,6 +72,12 @@
       "type": "double",
       "nullable": true,
       "metadata": {}
+    },
+    {
+      "name": "beta_ratio_sign",
+      "type": "double",
+      "nullable": true,
+      "metadata": {}
     }
   ]
 }
diff --git a/src/gentropy/method/colocalisation.py b/src/gentropy/method/colocalisation.py
@@ -85,6 +85,11 @@ def colocalise(
                     f.sum(f.col("clpp")).alias("clpp"),
                 )
                 .withColumn("colocalisationMethod", f.lit(cls.METHOD_NAME))
+                .join(overlapping_signals.calculate_beta_ratio(),
+                 ["leftStudyLocusId",
+                  "rightStudyLocusId",
+                   "chromosome"],
+                "left")
             ),
             _schema=Colocalisation.get_schema(),
         )
@@ -259,6 +264,11 @@ def colocalise(
                     "lH4bf",
                 )
                 .withColumn("colocalisationMethod", f.lit(cls.METHOD_NAME))
+                .join(overlapping_signals.calculate_beta_ratio(),
+                 ["leftStudyLocusId",
+                  "rightStudyLocusId",
+                   "chromosome"],
+                "left")
             ),
             _schema=Colocalisation.get_schema(),
         )