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dhimmel / learn

Machine learning and feature extraction for the Rephetio project
https://doi.org/10.15363/thinklab.d210
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auroc.tsv in 7-transform.ipynb #12

Closed maggielee1111 closed 9 months ago

maggielee1111 commented 10 months ago

Hi Daniel!

I'm trying to execute the notebook 7-transform.ipynb. In cell 2, there's a reference to the file data/auroc.tsv in the line summary_df = readr::read_tsv('data/auroc.tsv') but I couldn't locate this file in the repository.

However, I did find a file named auroc.tsv located at data/feature-performance/auroc.tsv. Its content seems different from what is expected in 7-transform.ipynb.

Could you please guide me on how to obtain the correct auroc.tsv file as referenced in 7-transform.ipynb notebook? I appreciate any assistance you can provide!

dhimmel commented 9 months ago

Hmm, I think data/auroc.tsv should be changed to data/feature-performance/primary-aurocs.tsv, which appears to match the schema of 7-transform.ipynb cell output 3.

Does that work?

Happy to accept a pull request with this file path change or other solution! Thanks for your interest.

maggielee1111 commented 9 months ago

Yes! It works fine and the data frame seems correct. However the funs_ function in cell 11 none = function(x) {return(1)} of 7-transform.ipynb was deprecated. Just created a pull request for changing aurocs.tsv to primary-aurocs.tsv.

dhimmel commented 9 months ago

Thanks for the PR. Feel free to also update dplyr::funs_ (in a new PR since I already merged https://github.com/dhimmel/learn/pull/13).