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Add functions update_GO_names, cap_names

Open TylerSagendorf opened this issue 1 year ago • 4 comments

update_GO_names pulls official GO term descriptions from the appropriate OBO file from the Gene Ontology Consortium. Uses data.table for fast replacement of values while merging, but can easily be rewritten with dplyr to remove that import. cap_names capitalizes the first letter of each term description unless there is special capitalization (e.g., "mRNA" would not be capitalized); improves visualizations.

TylerSagendorf avatar Aug 09 '22 17:08 TylerSagendorf

@igordot This addresses issue #19 . I thought this might be helpful, but feel free to scrap this if you don't think it is necessary.

TylerSagendorf avatar Aug 09 '22 17:08 TylerSagendorf

Thank you for doing this. This is a really nice enhancement and I am glad you shared the code. I still feel like this is outside the scope of the package and adds some extra dependencies, so I am not ready to merge it, but it's definitely helpful to have it here in case anyone is looking for such functionality.

igordot avatar Aug 09 '22 19:08 igordot

@igordot No worries. I'll probably make a helper package, then, that has some helper functions for this and the fgsea package. I'll let you know when I've had time to do that.

TylerSagendorf avatar Aug 11 '22 15:08 TylerSagendorf

A helper package is a great idea. I thought about suggesting that, but it seemed like an overkill for one function. Makes more sense as you add more functionality.

igordot avatar Aug 11 '22 16:08 igordot