Package index • PSMatch

All functions
`ConnectedComponents()` `ccMatrix()` `connectedComponents()` `length(<ConnectedComponents>)` `dims(<ConnectedComponents>)` `ncols(<ConnectedComponents>)` `nrows(<ConnectedComponents>)` `[`(<ConnectedComponents>,<integer>,<ANY>,<ANY>) `[`(<ConnectedComponents>,<logical>,<ANY>,<ANY>) `[`(<ConnectedComponents>,<numeric>,<ANY>,<ANY>) `prioritiseConnectedComponents()` `prioritizeConnectedComponents()` `adjacencyMatrix(<ConnectedComponents>)`	Connected components
`PSM()` `reduced()` `reduced<-`() `psmVariables()` `reducePSMs()` `adjacencyMatrix(<PSM>)`	A class for peptide-spectrum matches
`PSMatch-package` `PSMatch`	PSMatch: Handling and Managing Peptide Spectrum Matches
`makeAdjacencyMatrix()` `makePeptideProteinVector()` `plotAdjacencyMatrix()`	Convert to/from an adjacency matrix.
`calculateFragments(<character>,<missing>)`	Calculate ions produced by fragmentation with variable modifications
`describeProteins()` `describePeptides()`	Describe protein and peptide compositions
`filterPSMs()` `filterPsmDecoy()` `filterPsmRank()` `filterPsmShared()` `filterPsmFdr()`	Filter out unreliable PSMs.
`getAminoAcids()`	Amino acids
`getAtomicMass()`	Atomic mass.
`labelFragments()` `addFragments()`	labels MS2 Fragments
`plotSpectraPTM()`	Function to plot MS/MS spectra with PTMs

Reference