remove fragment matching lines from the create-synobj2 chunk
filter fragment.str in .filterIntensity (filterFragments) as well
use rank instead of sort(..., index.return=TRUE)
adjust confusionMatrix calculation to new rank
use pch=1 for number of peptides == 0
don't remove rows in filter{Non}UniqueMatches
fix Function assignment in .filterNonUniqueMatches
add warning if .filter{Non}UniqueMatches is used multiple times
clarify flatEMRT message (#67)
add crossmatching vignette