Label-free data analysis pipeline for optimal identification and quantitation

---

Documentation for package ‘synapter’ version 2.26.0

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

Help Pages

A B C D E F G I M P R S U V 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"
createUniquePeptideDbRds	Create an RDS file for the 'Unique Peptides Database'

-- D --

dim-method

Class "Synapter"

-- E --

estimateMasterFdr

Computes FDR for all possible final peptide combinations

-- F --

fileNames-method	Class '"MasterFdrResults"'
filterFragments	Class "Synapter"
filterFragments-method	Class "Synapter"
filterIdentPepScore	Class "Synapter"
filterIdentPepScore-method	Class "Synapter"
filterIdentPpmError	Class "Synapter"
filterIdentPpmError-method	Class "Synapter"
filterIdentProtFpr	Class "Synapter"
filterIdentProtFpr-method	Class "Synapter"
filterNonUniqueIdentMatches	Class "Synapter"
filterNonUniqueIdentMatches-method	Class "Synapter"
filterNonUniqueMatches	Class "Synapter"
filterNonUniqueMatches-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"
filterUniqueMatches	Class "Synapter"
filterUniqueMatches-method	Class "Synapter"
filterUniqueQuantDbPeptides	Class "Synapter"
filterUniqueQuantDbPeptides-method	Class "Synapter"
findEMRTs	Class "Synapter"
findEMRTs-method	Class "Synapter"
fragmentMatching	Class "Synapter"
fragmentMatching-method	Class "Synapter"
fragmentMatchingPerformance	Class "Synapter"
fragmentMatchingPerformance-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"
getFragmentMatchingPpmTolerance	Class "Synapter"
getFragmentMatchingPpmTolerance-method	Class "Synapter"
getGrid	Class "Synapter"
getGrid-method	Class "Synapter"
getGridDetails	Class "Synapter"
getGridDetails-method	Class "Synapter"
getIdentificationFragments	Class "Synapter"
getIdentificationFragments-method	Class "Synapter"
getIdentPpmError	Class "Synapter"
getIdentPpmError-method	Class "Synapter"
getImDiff	Class "Synapter"
getImDiff-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"
getQuantitationSpectra	Class "Synapter"
getQuantitationSpectra-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.
isCurrent-method	Class "Synapter"

-- 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"
modelIntensity	Class "Synapter"
modelIntensity-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"'
plotCumulativeNumberOfFragments	Class "Synapter"
plotCumulativeNumberOfFragments-method	Class "Synapter"
plotEMRTtable	Class "Synapter"
plotEMRTtable-method	Class "Synapter"
plotFdr	Class "Synapter"
plotFdr-method	Class "Synapter"
plotFeatures	Class "Synapter"
plotFeatures-method	Class "Synapter"
plotFragmentMatching	Plot fragment matching results.
plotFragmentMatching-method	Plot fragment matching results.
plotFragmentMatchingPerformance	Class "Synapter"
plotFragmentMatchingPerformance-method	Class "Synapter"
plotGrid	Class "Synapter"
plotGrid-method	Class "Synapter"
plotIntensity	Class "Synapter"
plotIntensity-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"

-- R --

requantify	Intensity requantification
requantify-method	Intensity requantification
rescaleForTop3	Rescale for TOP3
rescaleForTop3-method	Rescale for TOP3
rescueEMRTs	Class "Synapter"
rescueEMRTs-method	Class "Synapter"

-- S --

searchGrid	Class "Synapter"
searchGrid-method	Class "Synapter"
setBestGridParams	Class "Synapter"
setBestGridParams-method	Class "Synapter"
setFragmentMatchingPpmTolerance	Class "Synapter"
setFragmentMatchingPpmTolerance-method	Class "Synapter"
setIdentPpmError	Class "Synapter"
setIdentPpmError-method	Class "Synapter"
setImDiff	Class "Synapter"
setImDiff-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
synapterGuide	Opens the 'synapter' vignette
synapterPlgsAgreement	Synapter/PLGS Agreement
synapterPlgsAgreement-method	Synapter/PLGS Agreement
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
synergise1	Synergise identification and quantitation results
synergise2	Synergise identification and quantitation results
synergize	Synergise identification and quantitation results
synergize1	Synergise identification and quantitation results
synergize2	Synergise identification and quantitation results

-- U --

updateObject-method

Class "Synapter"

-- V --

validObject-method

Class "Synapter"

-- W --

writeFragmentLibrary	Merges final peptide files
writeFragmentLibrary-method	Merges final peptide files
writeIdentPeptides	Class "Synapter"
writeIdentPeptides-method	Class "Synapter"
writeMasterPeptides	Merges final peptide files
writeMasterPeptides-method	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"