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 |