Reduced the number of times the column medians are calculated

Arranged the files to the R pkg format, modified:
* get.pvals: I added arguments to then pass to getLimmaInput
* getLimmaInput: no longer calculates the column medians from samples it will discard, and now has the 'colmeds' argument.
* introduced getColmeds: calculates the column medians. This info can be saved and passed to get.pvals (which passes it to getLimmaInput) to avoid re-calculating this information.
* DESCRIPTION: added the list of pkg dependencies and bumped the version to 1.0.1
* Added the pdf of the vignette (but not the Rnw since I don't have it) to the pkg.
* Removed the weird . hidden character issue in the .R files