Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improve consistency of effect "beta" columns and "OR" columns #27

Open
mikegloudemans opened this issue May 4, 2020 · 0 comments
Open
Labels
code-base Maintaining reasonable and intuitive code compatibility Facilitating modular use with external tools munge Pertaining to the "munge" module

Comments

@mikegloudemans
Copy link
Owner

Add an assertion to munge script to make sure OR doesn't have negative value (if it does, it should simply be specified as an effect size instead)

In fact for simplicity...maybe ALL OR traits should actually be expressed in log form, to avoid annoyance downstream? We could just say in the coloc pipeline that we're going to use a beta? Could still include both, but beta should represent logOR, then could remove OR altogether from coloc script to avoid confusion, and tell people how to transform OR to beta...

But also, how does SE work when an OR is specified? I assume that's relative to the OR and not the log OR? Probably need to figure that out. Could probably still normalize OR somehow

@mikegloudemans mikegloudemans added munge Pertaining to the "munge" module compatibility Facilitating modular use with external tools code-base Maintaining reasonable and intuitive code labels May 4, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
code-base Maintaining reasonable and intuitive code compatibility Facilitating modular use with external tools munge Pertaining to the "munge" module
Projects
None yet
Development

No branches or pull requests

1 participant