refactor(L2GFeatureMatrix)!: streamline feature matrix management

docs/python_api/datasets/l2g_feature.md

@@ -2,7 +2,27 @@
 title: L2G Feature
 ---
 
-::: gentropy.method.l2g.feature_factory.L2GFeature
+## Abstract Class
+
+::: gentropy.dataset.l2g_feature.L2GFeature
+
+## Feature Classes
+
+### Derived from colocalisation
+
+::: gentropy.dataset.l2g_feature.EQtlColocClppMaximumFeature
+::: gentropy.dataset.l2g_feature.PQtlColocClppMaximumFeature
+::: gentropy.dataset.l2g_feature.SQtlColocClppMaximumFeature
+::: gentropy.dataset.l2g_feature.TuQtlColocClppMaximumFeature
+::: gentropy.dataset.l2g_feature.EQtlColocH4MaximumFeature
+::: gentropy.dataset.l2g_feature.PQtlColocH4MaximumFeature
+::: gentropy.dataset.l2g_feature.SQtlColocH4MaximumFeature
+::: gentropy.dataset.l2g_feature.TuQtlColocH4MaximumFeature
+
+### Derived from distance
+
+::: gentropy.dataset.l2g_feature.DistanceTssMinimumFeature
+::: gentropy.dataset.l2g_feature.DistanceTssMeanFeature
 
 ## Schema
 

docs/python_api/methods/l2g/feature_factory.md

@@ -2,6 +2,6 @@
 title: L2G Feature Factory
 ---
 
-::: gentropy.method.l2g.feature_factory.ColocalisationFactory
+::: gentropy.method.l2g.feature_factory.FeatureFactory
 
-::: gentropy.method.l2g.feature_factory.StudyLocusFactory
+::: gentropy.method.l2g.feature_factory.L2GFeatureInputLoader

src/gentropy/config.py

@@ -227,50 +227,16 @@ class LocusToGeneConfig(StepConfig):
     gene_interactions_path: str | None = None
     features_list: list[str] = field(
         default_factory=lambda: [
-            # average distance of all tagging variants to gene TSS
-            "distanceTssMean",
-            # minimum distance of all tagging variants to gene TSS
-            "distanceTssMinimum",
-            # maximum vep consequence score of the locus 95% credible set among all genes in the vicinity
-            "vepMaximumNeighborhood",
-            # maximum vep consequence score of the locus 95% credible set split by gene
-            "vepMaximum",
-            # mean vep consequence score of the locus 95% credible set among all genes in the vicinity
-            "vepMeanNeighborhood",
-            # mean vep consequence score of the locus 95% credible set split by gene
-            "vepMean",
-            # max clpp for each (study, locus, gene) aggregating over all eQTLs
-            "eqtlColocClppMaximum",
-            # max clpp for each (study, locus) aggregating over all eQTLs
-            "eqtlColocClppMaximumNeighborhood",
-            # max clpp for each (study, locus, gene) aggregating over all pQTLs
-            "pqtlColocClppMaximum",
-            # max clpp for each (study, locus) aggregating over all pQTLs
-            "pqtlColocClppMaximumNeighborhood",
-            # max clpp for each (study, locus, gene) aggregating over all sQTLs
-            "sqtlColocClppMaximum",
-            # max clpp for each (study, locus) aggregating over all sQTLs
-            "sqtlColocClppMaximumNeighborhood",
-            # max clpp for each (study, locus) aggregating over all tuQTLs
-            "tuqtlColocClppMaximum",
-            # max clpp for each (study, locus, gene) aggregating over all tuQTLs
-            "tuqtlColocClppMaximumNeighborhood",
-            # max log-likelihood ratio value for each (study, locus, gene) aggregating over all eQTLs
-            "eqtlColocLlrMaximum",
-            # max log-likelihood ratio value for each (study, locus) aggregating over all eQTLs
-            "eqtlColocLlrMaximumNeighborhood",
-            # max log-likelihood ratio value for each (study, locus, gene) aggregating over all pQTLs
-            "pqtlColocLlrMaximum",
-            # max log-likelihood ratio value for each (study, locus) aggregating over all pQTLs
-            "pqtlColocLlrMaximumNeighborhood",
-            # max log-likelihood ratio value for each (study, locus, gene) aggregating over all sQTLs
-            "sqtlColocLlrMaximum",
-            # max log-likelihood ratio value for each (study, locus) aggregating over all sQTLs
-            "sqtlColocLlrMaximumNeighborhood",
-            # max log-likelihood ratio value for each (study, locus, gene) aggregating over all tuQTLs
-            "tuqtlColocLlrMaximum",
-            # max log-likelihood ratio value for each (study, locus) aggregating over all tuQTLs
-            "tuqtlColocLlrMaximumNeighborhood",
+            # max CLPP for each (study, locus, gene) aggregating over a specific qtl type
+            "eQtlColocClppMaximum",
+            "pQtlColocClppMaximum",
+            "sQtlColocClppMaximum",
+            "tuQtlColocClppMaximum",
+            # max H4 for each (study, locus, gene) aggregating over a specific qtl type
+            "eQtlColocH4Maximum",
+            "pQtlColocH4Maximum",
+            "sQtlColocH4Maximum",
+            "tuQtlColocH4Maximum",
         ]
     )
     hyperparameters: dict[str, Any] = field(
@@ -283,6 +249,7 @@ class LocusToGeneConfig(StepConfig):
     wandb_run_name: str | None = None
     hf_hub_repo_id: str | None = "opentargets/locus_to_gene"
     download_from_hub: bool = True
+    write_feature_matrix: bool = True
     _target_: str = "gentropy.l2g.LocusToGeneStep"