adding regularization options to mlm - FZ - Githubissues

saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.

https://saezlab.github.io/decoupleR/

GNU General Public License v3.0

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adding regularization options to mlm - FZ #49

Closed fanzheng10 closed 2 years ago

fanzheng10 commented 2 years ago

require glmnet R package (put in "Suggests" in DESCRIPTION but can be moved to "Imports")
modify the statistic-mlm.R: adding the argument "regularization".

Benchmark performance for reference:

Ridge
PHP-unweighted: 0.647 (auc); 0.686 (pr_auc)
PHP-weighted: 0.669 (auc); 0.701 (pr_auc)
RNA_dorotheaABC: 0.623 (auc); 0.677 (pr_auc)

Lasso
PHP-unweighted: 0.608 (auc); 0.666 (pr_auc)
PHP-weighted: 0.664 (auc); 0.701 (pr_auc)
RNA_dorotheaABC: 0.617 (auc); 0.668 (pr_auc)