Used Rd2roxygen() from the Rd2roxygen package to parse all the Rd files.
Moved all the documentation to roxygen2 format using Rd2roxygen. Compiled all the documentation using document(derfinder, clean=TRUE) from the devtools package. Split the functions to one per file. Updated the DESCRIPTION file. Using @export to specify which functions to export (although some might be better kept as internal).
Merged with the new version of getLimmaInput that handles several comparison types
Updated the documentation of getLimmaInput for the 'comparison' argument
Merge pull request #2 from lcolladotor/master

Updated the documentation to use roxygen2