Define a class for the for major objects and clarify this a bit in mans and vignette

[SinomeM]

No description provided.

[SinomeM]

Also check that the major functions return objects of the correct classes

[SinomeM]

there is also this R CMD check WARNING

* checking S3 generic/method consistency ... WARNING
summary:
  function(object, ...)
summary.CNVresults:
  function(object, sample_list, markers, plots_path)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

[SinomeM]

Best thing is to define is.XXX and as.XXX functions