Save coefficients/hyperparameters for gene expression models - Githubissues

greenelab / mpmp

Multimodal Pan-cancer Mutation Prediction

BSD 3-Clause "New" or "Revised" License

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Save coefficients/hyperparameters for gene expression models #89

Closed jjc2718 closed 2 years ago

jjc2718 commented 2 years ago

As part of our revised manuscript (greenelab/mpmp-manuscript#46), we wanted to provide the coefficients (elastic net effect sizes) and hyperparameters (elastic net regularization strength + L1/L2 ratio) for the fit models using gene expression, for each gene in our cancer gene set; this PR fits the models on all the data and saves the coefficients/params.

Main additions in this PR:

Bash script to fit models for all genes: 07_train_final_classifiers/scripts/run_all_genes.sh
Notebook to assemble model info into .tsv files: 07_train_final_classifiers/collect_full_models.ipynb
Coefs/params files saved in data/final_models

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