addFragments	addFragments
adjacencyMatrix	adjacencyMatrix
adjacencyMatrix,ConnectedComponents	ConnectedComponents
adjacencyMatrix,ConnectedComponents-method	ConnectedComponents
adjacencyMatrix,PSM-method	PSM
calculateFragments	calculateFragments
calculateFragments,character,missing-method	calculateFragments
ccMatrix	ConnectedComponents
ConnectedComponents	ConnectedComponents
connectedComponents	ConnectedComponents
ConnectedComponents-class	ConnectedComponents
defaultNeutralLoss	calculateFragments
describePeptides	describeProteins
describeProteins	describeProteins
dims,ConnectedComponents	ConnectedComponents
dims,ConnectedComponents-method	ConnectedComponents
filterPsmDecoy	filterPSMs
filterPsmFdr	filterPSMs
filterPsmRank	filterPSMs
filterPSMs	filterPSMs
filterPsmShared	filterPSMs
getAminoAcids	getAminoAcids
getAtomicMass	getAtomicMass
length,ConnectedComponents	ConnectedComponents
length,ConnectedComponents-method	ConnectedComponents
makeAdjacencyMatrix	adjacencyMatrix
makePeptideProteinVector	adjacencyMatrix
ncols,ConnectedComponents	ConnectedComponents
ncols,ConnectedComponents-method	ConnectedComponents
nrows,ConnectedComponents	ConnectedComponents
nrows,ConnectedComponents-method	ConnectedComponents
plotAdjacencyMatrix	adjacencyMatrix
prioritiseConnectedComponents	ConnectedComponents
prioritizeConnectedComponents	ConnectedComponents
PSM	PSM
PSM,character	PSM
PSM,data.frame	PSM
PSM,PSM	PSM
PSM-class	PSM
PSMatch	PSMatch
psmVariables	PSM
readPSMs	PSM
reduced	PSM
reduced<-	PSM
reducePSMs	PSM
show,ConnectedComponents	ConnectedComponents
[,ConnectedComponents,integer,ANY,ANY	ConnectedComponents
[,ConnectedComponents,integer,ANY,ANY-method	ConnectedComponents
[,ConnectedComponents,logical,ANY,ANY	ConnectedComponents
[,ConnectedComponents,logical,ANY,ANY-method	ConnectedComponents
[,ConnectedComponents,numeric,ANY,ANY	ConnectedComponents
[,ConnectedComponents,numeric,ANY,ANY-method	ConnectedComponents
