move groundTruthIndices to utils.R
add .plotIonMobilitySummary
add argument equalCharge

Add argument equalCharge to compare only the ion mobility of equally charged
ions. The correct way would be to go back to the pep3d file and fetch the ion
mobility for the corresponding charge state from there. But because the current
results are not satisfying it seems to be not worth the additional effort.
extract ions that are used for identification (isFid == 1) from the Pep3D df instead of the first instance
reintroduce ion information for flatted MatchedEMRTs df
Merge branch 'master' into ionmobility

Conflicts:
	R/crossmatching-functions.R
move .groundTruthIndices to ionmobility-functions.R
add basic ion mobility vignette
add NEWS entry for ion mobility vignette
Merge pull request #58 from lgatto/ionmobility

summary plot for ion mobility