Firth penalized likelihood function in assocCoxPH

[ryshi06]

Hi there,

I am wondering is assocCoxph support firth's penalized likelihood function or other possible functions adjusting for monotone likelihood issues?

Thanks a lot!

Best,
Ruyu

[smgogarten]

No, it does not. While assocRegression has an option to use the Firth test (via the logistf package), assocCoxPH does not have that option. There is a package coxphf that would provide the test you're looking for, but I didn't know it existed until I looked it up just now to respond to your question.

This is not a feature I will have time to add anytime soon, but if you're interested in adding it to GWASTools yourself, you could submit a pull request.

[ryshi06]

Thanks for your reply. I 'll try the assocCoxPH first to decide whether I do need firth's correction. Thanks again!

Best,
Ruyu