Handling and Managing Peptide Spectrum Matches


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Documentation for package ‘PSMatch’ version 1.10.0

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PSMatch-package PSMatch: Handling and Managing Peptide Spectrum Matches
addFragments Adds 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
calculateFragments-method Calculate ions produced by fragmentation
ccMatrix Connected components
ConnectedComponents Connected components
connectedComponents Connected components
ConnectedComponents-class Connected components
defaultNeutralLoss Calculate ions produced by fragmentation
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.
length,ConnectedComponents Connected components
length-method Connected components
makeAdjacencyMatrix Convert to/from an adjacency matrix.
makePeptideProteinVector Convert to/from an adjacency matrix.
ncols,ConnectedComponents Connected components
ncols-method Connected components
nrows,ConnectedComponents Connected components
nrows-method Connected components
plotAdjacencyMatrix Convert to/from an adjacency matrix.
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