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--- |
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library_name: sklearn |
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tags: |
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- sklearn |
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- skops |
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- tabular-classification |
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model_format: skops |
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model_file: classifier.skops |
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widget: |
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- structuredData: |
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credibleSetConfidence: |
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- 0.75 |
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- 0.75 |
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- 0.75 |
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dhsPmtrCorrelationMean: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
|
dhsPmtrCorrelationMeanNeighbourhood: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
|
distanceFootprintMean: |
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- 0.8487144112586975 |
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- 0.9365111589431763 |
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- 0.9975032806396484 |
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distanceFootprintMeanNeighbourhood: |
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- 0.8487144112586975 |
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- 0.9365111589431763 |
|
- 0.9975032806396484 |
|
distanceSentinelFootprint: |
|
- 0.8487144112586975 |
|
- 0.9365111589431763 |
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- 0.9975032806396484 |
|
distanceSentinelFootprintNeighbourhood: |
|
- 0.8487144112586975 |
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- 0.9365111589431763 |
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- 0.9975032806396484 |
|
distanceSentinelTss: |
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- 0.8487144112586975 |
|
- 0.9257694482803345 |
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- 0.9975032806396484 |
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distanceSentinelTssNeighbourhood: |
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- 0.850220799446106 |
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- 0.9274126291275024 |
|
- 0.9992737770080566 |
|
distanceTssMean: |
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- 0.8487144112586975 |
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- 0.9257694482803345 |
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- 0.9975032806396484 |
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distanceTssMeanNeighbourhood: |
|
- 0.850220799446106 |
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- 0.9274126291275024 |
|
- 0.9992737770080566 |
|
eQtlColocClppMaximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
eQtlColocClppMaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
eQtlColocH4Maximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
eQtlColocH4MaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
enhTssCorrelationMean: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
enhTssCorrelationMeanNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
geneCount500kb: |
|
- 20.0 |
|
- 20.0 |
|
- 20.0 |
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pQtlColocClppMaximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pQtlColocClppMaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pQtlColocH4Maximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pQtlColocH4MaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pchicMean: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
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pchicMeanNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
proteinGeneCount500kb: |
|
- 8.0 |
|
- 8.0 |
|
- 8.0 |
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sQtlColocClppMaximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
sQtlColocClppMaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
sQtlColocH4Maximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
sQtlColocH4MaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
studyLocusId: |
|
- 005bc8624f8dd7f7c7bc63e651e9e59d |
|
- 005bc8624f8dd7f7c7bc63e651e9e59d |
|
- 005bc8624f8dd7f7c7bc63e651e9e59d |
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traitFromSourceMappedId: |
|
- EFO_0004612 |
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- EFO_0004612 |
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- EFO_0004612 |
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vepMaximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
vepMaximumNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
vepMean: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
vepMeanNeighbourhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
--- |
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# Model description |
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The locus-to-gene (L2G) model derives features to prioritise likely causal genes at each GWAS locus based on genetic and functional genomics features. The main categories of predictive features are: |
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- Distance: (from credible set variants to gene) |
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- Molecular QTL Colocalization |
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- Chromatin Interaction: (e.g., promoter-capture Hi-C) |
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- Variant Pathogenicity: (from VEP) |
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More information at: https://opentargets.github.io/gentropy/python_api/methods/l2g/_l2g/ |
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## Intended uses & limitations |
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[More Information Needed] |
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## Training Procedure |
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Gradient Boosting Classifier |
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### Hyperparameters |
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<details> |
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<summary> Click to expand </summary> |
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| Hyperparameter | Value | |
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|--------------------------|--------------| |
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| ccp_alpha | 0 | |
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| criterion | friedman_mse | |
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| init | | |
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| learning_rate | 0.1 | |
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| loss | log_loss | |
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| max_depth | 5 | |
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| max_features | | |
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| max_leaf_nodes | | |
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| min_impurity_decrease | 0.0 | |
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| min_samples_leaf | 5 | |
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| min_samples_split | 5 | |
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| min_weight_fraction_leaf | 0.0 | |
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| n_estimators | 100 | |
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| n_iter_no_change | | |
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| random_state | 42 | |
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| subsample | 1 | |
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| tol | 0.0001 | |
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| validation_fraction | 0.1 | |
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| verbose | 0 | |
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| warm_start | False | |
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</details> |
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# How to Get Started with the Model |
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To use the model, you can load it using the `LocusToGeneModel.load_from_hub` method. This will return a `LocusToGeneModel` object that can be used to make predictions on a feature matrix. |
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The model can then be used to make predictions using the `predict` method. |
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More information can be found at: https://opentargets.github.io/gentropy/python_api/methods/l2g/model/ |
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# Citation |
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https://doi.org/10.1038/s41588-021-00945-5 |
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# License |
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MIT |
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