File size: 2,164 Bytes
1220246 896bea9 9c77234 bbf73f3 1220246 9c77234 1220246 896bea9 bbf73f3 9c77234 bbf73f3 1220246 bbf73f3 1220246 bbf73f3 1220246 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 |
# Model description
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:
- Distance: (from credible set variants to gene)
- Molecular QTL Colocalization
- Chromatin Interaction: (e.g., promoter-capture Hi-C)
- Variant Pathogenicity: (from VEP)
More information at: https://opentargets.github.io/gentropy/python_api/methods/l2g/_l2g/
## Intended uses & limitations
[More Information Needed]
## Training Procedure
Gradient Boosting Classifier
### Hyperparameters
<details>
<summary> Click to expand </summary>
| Hyperparameter | Value |
|--------------------------|--------------|
| ccp_alpha | 0.0 |
| criterion | friedman_mse |
| init | |
| learning_rate | 0.1 |
| loss | log_loss |
| max_depth | 5 |
| max_features | |
| max_leaf_nodes | |
| min_impurity_decrease | 0.0 |
| min_samples_leaf | 1 |
| min_samples_split | 2 |
| min_weight_fraction_leaf | 0.0 |
| n_estimators | 100 |
| n_iter_no_change | |
| random_state | 42 |
| subsample | 1.0 |
| tol | 0.0001 |
| validation_fraction | 0.1 |
| verbose | 0 |
| warm_start | False |
</details>
# How to Get Started with the Model
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.
The model can then be used to make predictions using the `predict` method.
More information can be found at: https://opentargets.github.io/gentropy/python_api/methods/l2g/model/
# Citation
https://doi.org/10.1038/s41588-021-00945-5
# License
MIT
|