Handling and Managing Peptide Spectrum Matches

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Documentation for package ‘PSMatch’ version 1.13.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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