# Label-free data analysis pipeline for optimal identification and quantitation

## Documentation for package ‘synapter’ version 2.22.0

- 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"