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Check out the documentation for more information.
This Evaluator requests an interaction matrix readout for chromatin conformation in H1 cells (homo sapiens). It can be used with Predictors such as ORCA that have been trained on Hi-C data.
Included in Test_setChr8_Evaluator.sif :
- Scripts to process the data and send requests to Predictors in the GAME API
- ORCA evaluation support scripts from jzhoulab/orca
- Selene scripts from kathyxchen/selene
- Target values (large files) and hg38 reference genome
Prediction request details
- This evaluator requests predictions for 1M bp long sequences spanning chromosome 10 (138 sequences total) using hg38 annotations
/evaluator_data folder contents:
JSON request file
- Contains request metadata in the GAME API format
- Stores sequence start coordinates instead of full sequences to save space
- These coordinates are used by the main evaluator script to extract sequences
The folder also contains a python script to create the json file in case users want more details to reproduce the input data
Evaluation details:
- The 1Mbp long sequences will be pulled at runtime
- The Evaluator loads target Hi-C matrices and computes the Pearson r correlation between predictions and the measurements.
- This Evaluator can only evaluate the predictions from 1Mbp long sequences from the 1M resolution ORCA predictor for H1-ESC.
- Chromosome 10 is one of ORCA's validation set chromosomes
- Matrices with all NA predictions are excluded from correlation calculations
Additional information regarding ORCA and its evaluation can be found here: https://github.com/jzhoulab/orca
https://github.com/jzhoulab/orca_manuscript/blob/main/Model_performance.ipynb
Additional information regarding the GAME can be found here: https://github.com/de-Boer-Lab/Genomic-API-for-Model-Evaluation
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