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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: pickle |
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model_file: l2g_model_1006.pkl |
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widget: |
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- structuredData: |
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distanceTssMean: |
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- 0.1378757804632187 |
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- 0.004574988503009081 |
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- 0.01267080195248127 |
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distanceTssMinimum: |
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- 0.02554949000477791 |
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- 9.566087828716263e-05 |
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- 0.00206877407617867 |
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eqtlColocClppMaximum: |
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- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
eqtlColocClppMaximumNeighborhood: |
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- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
eqtlColocLlrMaximum: |
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- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
eqtlColocLlrMaximumNeighborhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pqtlColocClppMaximum: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
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pqtlColocClppMaximumNeighborhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pqtlColocLlrMaximum: |
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- 0.0 |
|
- 0.0 |
|
- 0.0 |
|
pqtlColocLlrMaximumNeighborhood: |
|
- 0.0 |
|
- 0.0 |
|
- 0.0 |
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sqtlColocClppMaximum: |
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- 0.0 |
|
- 0.0 |
|
- 0.0 |
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sqtlColocClppMaximumNeighborhood: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
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sqtlColocLlrMaximum: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
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sqtlColocLlrMaximumNeighborhood: |
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- 0.0 |
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- 0.0 |
|
- 0.0 |
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studyLocusId: |
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- -6454334657549107000 |
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- 6087706114048421000 |
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- -744015116205320800 |
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tuqtlColocClppMaximum: |
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- 0.0 |
|
- 0.0 |
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- 0.0 |
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tuqtlColocClppMaximumNeighborhood: |
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- 0.0 |
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- 0.0 |
|
- 0.0 |
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tuqtlColocLlrMaximum: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
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tuqtlColocLlrMaximumNeighborhood: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
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vepMaximum: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
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vepMaximumNeighborhood: |
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- 0.0 |
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- 0.0 |
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- 0.0 |
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vepMean: |
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- 0.0 |
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- 0.0 |
|
- 0.0 |
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vepMeanNeighborhood: |
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- 0.0 |
|
- 0.0 |
|
- 0.0 |
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--- |
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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 | 0.0 | |
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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 | 1 | |
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| min_samples_split | 2 | |
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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 | 1.0 | |
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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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