Label-free data analysis pipeline for optimal identification and quantitation

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Documentation for package ‘synapter’ version 1.6.0

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A B C D E F G I M P S W

synapter-package Combine label-free data for optimal identification and quantitation

-- A --

allComb Class '"MasterFdrResults"'
allComb-method Class '"MasterFdrResults"'
as.MSnSet.Synapter Class "Synapter"

-- B --

bestComb Class '"MasterFdrResults"'
bestComb-method Class '"MasterFdrResults"'

-- C --

class:MasterFdrResults Class '"MasterFdrResults"'
class:MasterPeptides Class '"MasterPeptides"'
class:Synapter Class "Synapter"

-- D --

dim-method Class "Synapter"

-- E --

estimateMasterFdr Computes FDR for all possible final peptide combinations

-- F --

fileNames-method Class '"MasterFdrResults"'
filterIdentPepScore Class "Synapter"
filterIdentPepScore-method Class "Synapter"
filterIdentPpmError Class "Synapter"
filterIdentPpmError-method Class "Synapter"
filterIdentProtFpr Class "Synapter"
filterIdentProtFpr-method Class "Synapter"
filterPeptideLength Class "Synapter"
filterPeptideLength-method Class "Synapter"
filterQuantPepScore Class "Synapter"
filterQuantPepScore-method Class "Synapter"
filterQuantPpmError Class "Synapter"
filterQuantPpmError-method Class "Synapter"
filterQuantProtFpr Class "Synapter"
filterQuantProtFpr-method Class "Synapter"
filterUniqueDbPeptides Class "Synapter"
filterUniqueDbPeptides-method Class "Synapter"
filterUniqueIdentDbPeptides Class "Synapter"
filterUniqueIdentDbPeptides-method Class "Synapter"
filterUniqueQuantDbPeptides Class "Synapter"
filterUniqueQuantDbPeptides-method Class "Synapter"
findEMRTs Class "Synapter"
findEMRTs-method Class "Synapter"

-- G --

getBestGridParams Class "Synapter"
getBestGridParams-method Class "Synapter"
getBestGridValue Class "Synapter"
getBestGridValue-method Class "Synapter"
getEMRTtable Class "Synapter"
getEMRTtable-method Class "Synapter"
getGrid Class "Synapter"
getGrid-method Class "Synapter"
getGridDetails Class "Synapter"
getGridDetails-method Class "Synapter"
getIdentPpmError Class "Synapter"
getIdentPpmError-method Class "Synapter"
getLog Class "Synapter"
getLog-method Class "Synapter"
getLowessSpan Class "Synapter"
getLowessSpan-method Class "Synapter"
getPepNumbers Class "Synapter"
getPepNumbers-method Class "Synapter"
getPepScoreFdr Class "Synapter"
getPepScoreFdr-method Class "Synapter"
getPpmErrorQs Class "Synapter"
getPpmErrorQs-method Class "Synapter"
getProtFpr Class "Synapter"
getProtFpr-method Class "Synapter"
getQuantPpmError Class "Synapter"
getQuantPpmError-method Class "Synapter"
getRtNsd Class "Synapter"
getRtNsd-method Class "Synapter"
getRtQs Class "Synapter"
getRtQs-method Class "Synapter"

-- I --

inputFiles Class "Synapter"
inputFiles-method Class "Synapter"
inspectPeptideScores Inspect peptide scores.

-- M --

makeMaster Merges final peptide files
masterFdr Class '"MasterFdrResults"'
masterFdr-method Class '"MasterFdrResults"'
MasterFdrResults Class '"MasterFdrResults"'
MasterFdrResults-class Class '"MasterFdrResults"'
MasterPeptides-class Class '"MasterPeptides"'
mergePeptides Class "Synapter"
mergePeptides-method Class "Synapter"
modelRt Class "Synapter"
modelRt-method Class "Synapter"

-- P --

performance Class "Synapter"
performance-method Class "Synapter"
performance2 Class "Synapter"
performance2-method Class "Synapter"
plot-method Class '"MasterFdrResults"'
plotEMRTtable Class "Synapter"
plotEMRTtable-method Class "Synapter"
plotFdr Class "Synapter"
plotFdr-method Class "Synapter"
plotFeatures Class "Synapter"
plotFeatures-method Class "Synapter"
plotGrid Class "Synapter"
plotGrid-method Class "Synapter"
plotPepScores Class "Synapter"
plotPepScores-method Class "Synapter"
plotPpmError Class "Synapter"
plotPpmError-method Class "Synapter"
plotRt Class "Synapter"
plotRt-method Class "Synapter"
plotRtDiffs Class "Synapter"
plotRtDiffs-method Class "Synapter"

-- S --

searchGrid Class "Synapter"
searchGrid-method Class "Synapter"
setBestGridParams Class "Synapter"
setBestGridParams-method Class "Synapter"
setIdentPpmError Class "Synapter"
setIdentPpmError-method Class "Synapter"
setLowessSpan Class "Synapter"
setLowessSpan-method Class "Synapter"
setPepScoreFdr Class "Synapter"
setPepScoreFdr-method Class "Synapter"
setPpmError Class "Synapter"
setPpmError-method Class "Synapter"
setProtFpr Class "Synapter"
setProtFpr-method Class "Synapter"
setQuantPpmError Class "Synapter"
setQuantPpmError-method Class "Synapter"
setRtNsd Class "Synapter"
setRtNsd-method Class "Synapter"
show-method Class '"MasterFdrResults"'
show-method Class '"MasterPeptides"'
show-method Class "Synapter"
showFdrStats Class "Synapter"
showFdrStats-method Class "Synapter"
Synapter Class "Synapter"
synapter Combine label-free data for optimal identification and quantitation
synapterGUI Launch the synapter GUI
synapterGuide Opens the 'synapter' vignette
synapterTiny Loads a small test data for the 'synapter' package
synapterTinyData Loads a small test data for the 'synapter' package
synergise Synergise identification and quantitation results
synergize Synergise identification and quantitation results

-- W --

writeIdentPeptides Class "Synapter"
writeIdentPeptides-method Class "Synapter"
writeMasterPeptides Merges final peptide files
writeMatchedEMRTs Class "Synapter"
writeMatchedEMRTs-method Class "Synapter"
writeMergedPeptides Class "Synapter"
writeMergedPeptides-method Class "Synapter"
writeQuantPeptides Class "Synapter"
writeQuantPeptides-method Class "Synapter"