docs(warnings): Remove warnings related to documentation

[tonywu1999]

Motivation and Context

To make development easier, we should remove all existing warnings so that it's easy to spot if a change produced more warnings than before. Also, these warnings are quick fixes related to missing documentation that should be addressed.

There are 3 warnings for this package:

❯ checking S3 generic/method consistency ... WARNING
  as.data.table:
    function(x, keep.rownames, ...)
  as.data.table.MSstatsValidated:
    function(x)
  
  as.data.frame:
    function(x, row.names, optional, ...)
  as.data.frame.MSstatsValidated:
    function(x)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

❯ checking for missing documentation entries ... WARNING
  Undocumented S4 methods:
    generic 'getInputFile' and siglist 'MSstatsPhilosopherFiles'
  All user-level objects in a package (including S4 classes and methods)
  should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking Rd \usage sections ... WARNING
  Undocumented arguments in documentation object 'MSstatsClean'
    ‘channels’
  
  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.

Changes

• Warning 1: Added ... as a parameter for as.data.table.MSstatsValidated and as.data.frame.MSstatsValidated to make sure generic parameters matched method parameters.
• Warning 2: Added documentation for getInputFile where the input class is MSstatsPhilosopherFiles
• Warning 3: Fixed spelling error of parameter in documentation

Testing

1. Ran devtools::document() and devtools::check(document = FALSE) and they both succeed.
2. Dry Run Build produces 0 warnings

Checklist Before Requesting a Review

• I have read this repository's contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

[mstaniak]

Thanks!