search

smgogarten / GWASTools

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis
https://bioconductor.org/packages/GWASTools
16 stars 6 forks source link

Firth penalized likelihood function in assocCoxPH #8

Open ryshi06 opened 3 years ago

ryshi06 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

Best, Ruyu