Add function documentation

[awasyn]

Document parameters

What kind of change(s) are included?

• [R-pkg] Status check #2

• 🐞[BUG] fix check bugs #33

• Bug fix (fixes check).(devtools::document()) Should be cleaned when merged with: Add parameter definitions to summarize.R #41

• Enhancement (documentation).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• I have read and followed the CONTRIBUTING.md guidelines.
• I have searched for existing content to ensure this is not a duplicate.
• I have performed a self-review of these additions (including spelling, grammar, and related).
• I have added comments to my code to help provide understanding.
• I have added a test which covers the code changes found within this PR.
• I have deleted all non-relevant text in this pull request template.
• Reviewer assignment: Tag a relevant team member to review and approve the changes.

@the-mayer

[the-mayer]

@awasyn , can you double check this example code?

[awasyn]

Thanks. I will run example again.

[awasyn]

Done.

[the-mayer]

I'm still seeing an R-CMD check error when running this example:

❯ checking examples ... [14s/15s] ERROR
  Running examples in ‘MolEvolvR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: reverseOperonSeq
  > ### Title: reverseOperon: Reverse the Direction of Operons in Genomic
  > ###   ContextSeq
  > ### Aliases: reverseOperonSeq
  > 
  > ### ** Examples
  > 
  > # Example genomic context data frame
  > prot <- data.frame(GenContext = c("A>B", "C<D", "E=F*G", "H>I"))
  > reversed_prot <- reverseOperonSeq(prot)
  Error in ge[[x]] : subscript out of bounds
  Calls: reverseOperonSeq -> lapply -> FUN -> straightenOperonSeq
  Execution halted

Using the example data defined in prot the error occurs during the lapply operation @line 137 as ge has length 0 due to the previous subset operation.

[the-mayer]

Excellent work adding to the package documentation! I've made a few requests for changes (picked some representative examples, but changes should be made throughout).

Overall this looks great and is another step towards enabling the CI in #34

[the-mayer]

I've disabled the reverseOperonSeq() example for now and converted to a new issue so that other changes may be merged. Thanks @awasyn !

[awasyn]

Thanks @the-mayer , sorry for the delay. I was finishing my final application for the internship.
However i have recently tried to pass different examples and g[[x]] is empty every time. I'll add this clean up to my milestones. Error handling and refactoring the function..