invoked Yihui Xie's formatR() to make it a little easier to read.

[abelew]

Greetings,
I looked over the manuscript and code with great interest. I think there are some super-neat ideas, but wanted the code to be a bit easier to follow; thus I did the following.
I would not necessarily suggest that you actually merge this pull request, but check it out and see if it is useful. If you are interested, there are a few other minor changes I would consider in order to make this a bit more robust, especially if you wish to send this to cran. But on the other hand, you might look at this as a bunch of stupid changes and that is understandable.

Also I dropped in some stub roxygen docstrings and attempted to
standardize how :: is used in the codebase. Ideally, I did nothing to
change the function or action of the code.

[ruy204]

Hi abelew, thank you for your input! These are valuable points, and I am also working towards cleaning up the code and making them more robust, consistent and read-able. This is also my first time to create an R package, so please feel free to give more comments/suggestions.

[abelew]

No worries. Some folks I work with are interested in potentially using your package. There are a couple of oddities which might make it difficult. Most importantly the support_list.rda; as I hope to use other species/strains and I do not understand these data structures.
I did read the data.R and noted the docstrings; it seems that the cluster information should be trivially extracted from species/strain specific gff files and/or some existing annotation data.
I am thinking therefore to modify the tallyprepfun() to handle arbitrary annotation data. I do not yet know how to create similar data structures to fill in 'nonPermissiveTA' and 'homo'.