fix: small fixes in susie defaults (#552)

opentargets · Mar 21, 2024 · dee3085 · dee3085
1 parent 650bb2e
commit dee3085
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/src/gentropy/method/susie_inf.py b/src/gentropy/method/susie_inf.py
@@ -34,7 +34,7 @@ def susie_inf(  # noqa: C901
         ssq_range: tuple[float, float] = (0, 1),
         pi0: np.ndarray | None = None,
         est_sigmasq: bool = True,
-        est_tausq: bool = True,
+        est_tausq: bool = False,
         sigmasq: float = 1,
         tausq: float = 0,
         sigmasq_range: tuple[float, float] | None = None,
@@ -399,7 +399,7 @@ def g(x: float) -> float:
     def cred_inf(
         PIP: np.ndarray,
         n: int = 100_000,
-        coverage: float = 0.9,
+        coverage: float = 0.99,
         purity: float = 0.5,
         LD: np.ndarray | None = None,
         V: np.ndarray | None = None,

diff --git a/tests/gentropy/method/test_susie_inf.py b/tests/gentropy/method/test_susie_inf.py
@@ -16,7 +16,7 @@ def test_SUSIE_inf_lbf_moments(
         ld = sample_data_for_susie_inf[0]
         z = sample_data_for_susie_inf[1]
         lbf_moments = sample_data_for_susie_inf[2]
-        susie_output = SUSIE_inf.susie_inf(z=z, LD=ld, method="moments")
+        susie_output = SUSIE_inf.susie_inf(z=z, LD=ld, est_tausq=True, method="moments")
         lbf_calc = susie_output["lbf_variable"][:, 0]
         assert np.allclose(
             lbf_calc, lbf_moments
@@ -29,7 +29,7 @@ def test_SUSIE_inf_lbf_mle(
         ld = sample_data_for_susie_inf[0]
         z = sample_data_for_susie_inf[1]
         lbf_mle = sample_data_for_susie_inf[3]
-        susie_output = SUSIE_inf.susie_inf(z=z, LD=ld, method="MLE")
+        susie_output = SUSIE_inf.susie_inf(z=z, LD=ld, est_tausq=True, method="MLE")
         lbf_calc = susie_output["lbf_variable"][:, 0]
         assert np.allclose(
             lbf_calc, lbf_mle, atol=1e-1
@@ -41,6 +41,10 @@ def test_SUSIE_inf_cred(
         """Test of SuSiE-inf credible set generator."""
         ld = sample_data_for_susie_inf[0]
         z = sample_data_for_susie_inf[1]
-        susie_output = SUSIE_inf.susie_inf(z=z, LD=ld)
+        susie_output = SUSIE_inf.susie_inf(
+            z=z,
+            LD=ld,
+            est_tausq=True,
+        )
         cred = SUSIE_inf.cred_inf(susie_output["PIP"], LD=ld)
         assert cred[0] == [5]