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greenelab / pancancer-evaluation

Evaluating genome-wide prediction of driver mutations using pan-cancer data
BSD 3-Clause "New" or "Revised" License
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Add more genes and random features baseline to cancer type experiments #49

Closed jjc2718 closed 2 years ago

jjc2718 commented 2 years ago

As a continuation of #48, we ran the same experiments for more genes, and added random feature selection (of the same number of features) as a baseline.

General results are similar to what we saw before - PTEN is an example of a gene where our feature selection method (median_f_test) works well for non-carcinoma cancer types:

image

Some other genes we tried (RB1, BRAF) don't seem to work as well, though.

I also added a script at 02_cancer_type_classification/scripts/run_fs_for_genes.sh to run 02_cancer_type_classification/plot_univariate_fs_results.ipynb for all the genes we looked at and save the resulting plots (I didn't track the plots here, just locally).

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