Revision of qcscore_model_spe branch

[Copilot]

• Fixed some issues with QS computation with custom formula;
• updated QC functions documentation;
• added more customizable settings to plot functions;
• function name standardization to Quality Score (QScore);
• added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
• updated vignettes.

[drighelli]

@copilot fix warning and note coming from workflows!
Check consistencies of the function arguments in the function code itself!

❯ checking Rd \usage sections ... WARNING
  Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
    ‘csize’ ‘calpha’
  
  Functions with \usage entries need to have the appropriate \alias
  entries, and all their arguments documented.
  The \usage entries must correspond to syntactically valid R code.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking R code for possible problems ... NOTE
  computeQScore: no visible global function definition for ‘terms’
  Undefined global functions or variables:
    terms
  Consider adding
    importFrom("stats", "terms")
  to your NAMESPACE file.

[Copilot]

@copilot fix warning and note coming from workflows!
Check consistencies of the function arguments in the function code itself!

...

Fixed both issues in commit Fix R CMD check WARNING and NOTE:

1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).

2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.