fix: add scQTLs into coloc features (#833)

* fix: add scQTLs into coloc features * fix: include single cell qtls in the list of valid study types --------- Co-authored-by: Irene López <irene.lopezs@protonmail.com>
opentargets · Oct 22, 2024 · de4627f · de4627f
1 parent 7b20d55
commit de4627f
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Showing 2 changed files with 14 additions and 9 deletions.
diff --git a/src/gentropy/dataset/colocalisation.py b/src/gentropy/dataset/colocalisation.py
@@ -62,7 +62,12 @@ def extract_maximum_coloc_probability_per_region_and_gene(
 
         valid_qtls = list(
             set(EqtlCatalogueStudyIndex.method_to_study_type_mapping.values())
-        )
+        ) + [
+            f"sc{qtl}"
+            for qtl in set(
+                EqtlCatalogueStudyIndex.method_to_study_type_mapping.values()
+            )
+        ]
 
         if filter_by_qtls:
             filter_by_qtls = (

diff --git a/src/gentropy/dataset/l2g_features/colocalisation.py b/src/gentropy/dataset/l2g_features/colocalisation.py
@@ -211,7 +211,7 @@ def compute(
         """
         colocalisation_method = "ECaviar"
         colocalisation_metric = "clpp"
-        qtl_type = "eqtl"
+        qtl_type = ["eqtl", "sceqtl"]
 
         return cls(
             _df=convert_from_wide_to_long(
@@ -260,7 +260,7 @@ def compute(
         """
         colocalisation_method = "ECaviar"
         colocalisation_metric = "clpp"
-        qtl_type = "eqtl"
+        qtl_type = ["eqtl", "sceqtl"]
 
         return cls(
             _df=convert_from_wide_to_long(
@@ -393,7 +393,7 @@ def compute(
         """
         colocalisation_method = "ECaviar"
         colocalisation_metric = "clpp"
-        qtl_types = ["sqtl", "tuqtl"]
+        qtl_types = ["sqtl", "tuqtl", "scsqtl", "sctuqtl"]
         return cls(
             _df=convert_from_wide_to_long(
                 common_colocalisation_feature_logic(
@@ -441,7 +441,7 @@ def compute(
         """
         colocalisation_method = "ECaviar"
         colocalisation_metric = "clpp"
-        qtl_types = ["sqtl", "tuqtl"]
+        qtl_types = ["sqtl", "tuqtl", "scsqtl", "sctuqtl"]
         return cls(
             _df=convert_from_wide_to_long(
                 common_neighbourhood_colocalisation_feature_logic(
@@ -483,7 +483,7 @@ def compute(
         """
         colocalisation_method = "Coloc"
         colocalisation_metric = "h4"
-        qtl_type = "eqtl"
+        qtl_type = ["eqtl", "sceqtl"]
         return cls(
             _df=convert_from_wide_to_long(
                 common_colocalisation_feature_logic(
@@ -531,7 +531,7 @@ def compute(
         """
         colocalisation_method = "Coloc"
         colocalisation_metric = "h4"
-        qtl_type = "eqtl"
+        qtl_type = ["eqtl", "sceqtl"]
         return cls(
             _df=convert_from_wide_to_long(
                 common_neighbourhood_colocalisation_feature_logic(
@@ -663,7 +663,7 @@ def compute(
         """
         colocalisation_method = "Coloc"
         colocalisation_metric = "h4"
-        qtl_types = ["sqtl", "tuqtl"]
+        qtl_types = ["sqtl", "tuqtl", "scsqtl", "sctuqtl"]
         return cls(
             _df=convert_from_wide_to_long(
                 common_colocalisation_feature_logic(
@@ -711,7 +711,7 @@ def compute(
         """
         colocalisation_method = "Coloc"
         colocalisation_metric = "h4"
-        qtl_types = ["sqtl", "tuqtl"]
+        qtl_types = ["sqtl", "tuqtl", "scsqtl", "sctuqtl"]
         return cls(
             _df=convert_from_wide_to_long(
                 common_neighbourhood_colocalisation_feature_logic(