throw warning if the user already filtered by CX

Throws a warning if the column "Function.0" is already present in the
CrossMatching data.frame to show the user that he won't get the expected results
if he runs filterMatchedEMRTsUsingCrossMatching multiple times on the same
synapter object.
add "what" argument to cross match filter

Adds a "what" argument to filterMatchedEMRTsUsingCrossMatching. This argument
could be `c("non-unique", "all")`. For "all" all rows that are not matching the
criteria are remove from the MatchedEMRTs data.frame. "non-unique" just turns
non unique matches into unique ones, without removing anything.
add plotCrossMatchingPerformance
add cx columns to MatchedEMRTs data.frame

Adds the columns "spectrum.identXfragments.quant",
"spectrum.quantXfragments.ident" and "fragments.identXfragments.quant" to the
MatchedEMRTs data.frame.
Merge pull request #64 from lgatto/cxPerformance

cross matching performance plots