Arranged the files like an R pkg. Added the manual files from a different derfinder version AF provided. Updated the description file with all the dependcies I found.
Added more arguments passed to get.pvals which are then used in getLimmaInput
getLimmaInput no longer reads the medians from the columns that it will discard
Modified how getLimmaInput() and get.pvals() calculate the column medians by introducing getColmeds() whose output can be saved once and avoid having to calculate it many times
Fixed a typo on the description
Updated the derfinder man page
Added a help file for getColmeds and updated the documentation for get.pvals and getLimmaInput. Will send AF a pull request
Fixed get.pvals so the permutation is appropriately transmited to the adjustvars and colsubset