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ByrumLab / proteoDA

GNU General Public License v3.0
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vignette edits #230

Closed tjthurman closed 1 year ago

tjthurman commented 1 year ago

Some changes to the vignette. Some are edits, some are suggestions. Can update the PR after review based on what you want to keep or not:

Necessary changes: some wording fixes here and there, and a correction in the section on the 1/0/-1 columns in the results. Those are already in the results objects in R, they aren't only output by the table writing functions

Suggestions: I think we should simplify the function calls and generally not include arguments with defaults or that are extraneous. Those are explained in their function reference pages, but aren't clear in the tutorial. If we want to keep some, I think we definitely should not include arguments where we specify the default NULL, like in the DAList() function. I think this is confusing to users (why are we specifying arguments with no value?).

tjthurman commented 1 year ago

So, keep them all, even the NULLs?

ByrumLab commented 1 year ago

Yes, just the way I had it.