Final SHRD code, plus unrelated bug fixes from Max and Ding

Huntsmanlab / utanos

Utilities for doing analysis on shallow WGS data

https://huntsmanlab.github.io/utanos/

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Final SHRD code, plus unrelated bug fixes from Max and Ding #70

Closed brandenjlynch closed 3 months ago

genomaxx commented 3 months ago

The file naming convention for the sHRD functions differs from the rest of the package. I like the 'shrd_' prefix to those files because it allows for easy reference. Not sure about the rest having longer titles and more underscores. Any strong opinions? The tidyverse style guide (https://style.tidyverse.org/package-files.html), and the R packages book (https://r-pkgs.org/code.html) don't appear to have strong recommendations.

genomaxx commented 3 months ago

I agree that this one should be a merge commit. Definitely would be nice to rollback easily if necessary.

genomaxx commented 3 months ago

Broader convo/consideration I think we need to file as an 'Issue': We are exporting a ton of these shallowHRD functions to the namespace. Do they all need to user facing? Most depend on one another and are not useful in isolation. I doubt a user will ever want to touch most of them. Food for thought.