Fix normalization of the penetrance table so the NULL model works

HallLab · Apr 23, 2021 · c2a73d8 · c2a73d8
1 parent eebe6c0
commit c2a73d8
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/pandas_genomics/sim/BAMS.py b/pandas_genomics/sim/BAMS.py
@@ -223,7 +223,9 @@ def generate_case_control(
         if (pen_table.min() != 0) or (pen_table.max() != 1):
             pen_table_min = pen_table.min()
             pen_table_range = pen_table.max() - pen_table_min
-            pen_table = (pen_table - pen_table_min) / pen_table_range
+            if pen_table_range > 0:
+                pen_table = (pen_table - pen_table_min) / pen_table_range
+                # Otherwise the penetrance table is flat, i.e. a null model
 
         # Create table of Prob(GT) based on MAF, assuming HWE
         prob_snp1 = np.array([(1 - maf1) ** 2, 2 * maf1 * (1 - maf1), (maf1) ** 2])

diff --git a/tests/simulation/test_biallelic_sim.py b/tests/simulation/test_biallelic_sim.py
@@ -45,3 +45,11 @@ def test():
 
     # Test quantitative sim
     simulated_df_quant = test_sim.generate_quantitative()
+
+
+def test_null():
+    bas = BAMS(PenetranceTables.NULL)
+    simulated = bas.generate_case_control(10000, 1000, 0.1, 0.1)
+    # maf should be similar to the specified one despite a large fraction of cases
+    # specifically assert it is within 5%
+    assert abs(0.1 - simulated["SNP1"].genomics.maf) / 0.1 < 0.05