synapter-package	synapter-package
allComb	MasterFdrResults-class
allComb,MasterFdrResults-method	MasterFdrResults-class
as.MSnSet.Synapter	Synapter
bestComb	MasterFdrResults-class
bestComb,MasterFdrResults-method	MasterFdrResults-class
class:MasterFdrResults	MasterFdrResults-class
class:MasterPeptides	MasterPeptides-class
class:Synapter	Synapter
createUniquePeptideDbRds	createUniquePeptideDbRds
dim,Synapter-method	Synapter
estimateMasterFdr	estimateMasterFdr
fileNames,MasterFdrResults-method	MasterFdrResults-class
filterFragments	Synapter
filterFragments,Synapter-method	Synapter
filterIdentPepScore	Synapter
filterIdentPepScore,Synapter-method	Synapter
filterIdentPpmError	Synapter
filterIdentPpmError,Synapter-method	Synapter
filterIdentProtFpr	Synapter
filterIdentProtFpr,Synapter-method	Synapter
filterNonUniqueIdentMatches	Synapter
filterNonUniqueIdentMatches,Synapter-method	Synapter
filterNonUniqueMatches	Synapter
filterNonUniqueMatches,Synapter-method	Synapter
filterPeptideLength	Synapter
filterPeptideLength,Synapter-method	Synapter
filterQuantPepScore	Synapter
filterQuantPepScore,Synapter-method	Synapter
filterQuantPpmError	Synapter
filterQuantPpmError,Synapter-method	Synapter
filterQuantProtFpr	Synapter
filterQuantProtFpr,Synapter-method	Synapter
filterUniqueDbPeptides	Synapter
filterUniqueDbPeptides,Synapter-method	Synapter
filterUniqueIdentDbPeptides	Synapter
filterUniqueIdentDbPeptides,Synapter-method	Synapter
filterUniqueMatches	Synapter
filterUniqueMatches,Synapter-method	Synapter
filterUniqueQuantDbPeptides	Synapter
filterUniqueQuantDbPeptides,Synapter-method	Synapter
findEMRTs	Synapter
findEMRTs,Synapter-method	Synapter
fragmentMatching	Synapter
fragmentMatching,Synapter-method	Synapter
fragmentMatchingPerformance	Synapter
fragmentMatchingPerformance,Synapter-method	Synapter
getBestGridParams	Synapter
getBestGridParams,Synapter-method	Synapter
getBestGridValue	Synapter
getBestGridValue,Synapter-method	Synapter
getEMRTtable	Synapter
getEMRTtable,Synapter-method	Synapter
getFragmentMatchingPpmTolerance	Synapter
getFragmentMatchingPpmTolerance,Synapter-method	Synapter
getGrid	Synapter
getGrid,Synapter-method	Synapter
getGridDetails	Synapter
getGridDetails,Synapter-method	Synapter
getIdentificationFragments	Synapter
getIdentificationFragments,Synapter-method	Synapter
getIdentPpmError	Synapter
getIdentPpmError,Synapter-method	Synapter
getImDiff	Synapter
getImDiff,Synapter-method	Synapter
getLog	Synapter
getLog,Synapter-method	Synapter
getLowessSpan	Synapter
getLowessSpan,Synapter-method	Synapter
getPepNumbers	Synapter
getPepNumbers,Synapter-method	Synapter
getPepScoreFdr	Synapter
getPepScoreFdr,Synapter-method	Synapter
getPpmErrorQs	Synapter
getPpmErrorQs,Synapter-method	Synapter
getProtFpr	Synapter
getProtFpr,Synapter-method	Synapter
getQuantitationSpectra	Synapter
getQuantitationSpectra,Synapter-method	Synapter
getQuantPpmError	Synapter
getQuantPpmError,Synapter-method	Synapter
getRtNsd	Synapter
getRtNsd,Synapter-method	Synapter
getRtQs	Synapter
getRtQs,Synapter-method	Synapter
inputFiles	Synapter
inputFiles,Synapter-method	Synapter
inspectPeptideScores	inspectPeptideScores
isCurrent,Synapter-method	Synapter
makeMaster	makeMaster
masterFdr	MasterFdrResults-class
masterFdr,MasterFdrResults-method	MasterFdrResults-class
MasterFdrResults	MasterFdrResults-class
MasterFdrResults-class	MasterFdrResults-class
MasterPeptides-class	MasterPeptides-class
mergePeptides	Synapter
mergePeptides,Synapter-method	Synapter
modelIntensity	Synapter
modelIntensity,Synapter-method	Synapter
modelRt	Synapter
modelRt,Synapter-method	Synapter
performance	Synapter
performance,Synapter-method	Synapter
performance2	Synapter
performance2,Synapter-method	Synapter
plot,MasterFdrResults,missing-method	MasterFdrResults-class
plotCumulativeNumberOfFragments	Synapter
plotCumulativeNumberOfFragments,Synapter-method	Synapter
plotEMRTtable	Synapter
plotEMRTtable,Synapter-method	Synapter
plotFdr	Synapter
plotFdr,Synapter-method	Synapter
plotFeatures	Synapter
plotFeatures,Synapter-method	Synapter
plotFragmentMatching	plotCrossMatching
plotFragmentMatching,Synapter-method	plotCrossMatching
plotFragmentMatchingPerformance	Synapter
plotFragmentMatchingPerformance,Synapter-method	Synapter
plotGrid	Synapter
plotGrid,Synapter-method	Synapter
plotIntensity	Synapter
plotIntensity,Synapter-method	Synapter
plotPepScores	Synapter
plotPepScores,Synapter-method	Synapter
plotPpmError	Synapter
plotPpmError,Synapter-method	Synapter
plotRt	Synapter
plotRt,Synapter-method	Synapter
plotRtDiffs	Synapter
plotRtDiffs,Synapter-method	Synapter
requantify	requantify
requantify,MSnSet-method	requantify
rescaleForTop3	rescaleForTop3
rescaleForTop3,MSnSet,MSnSet-method	rescaleForTop3
rescueEMRTs	Synapter
rescueEMRTs,Synapter-method	Synapter
searchGrid	Synapter
searchGrid,Synapter-method	Synapter
setBestGridParams	Synapter
setBestGridParams,Synapter-method	Synapter
setFragmentMatchingPpmTolerance	Synapter
setFragmentMatchingPpmTolerance,Synapter-method	Synapter
setIdentPpmError	Synapter
setIdentPpmError,Synapter-method	Synapter
setImDiff	Synapter
setImDiff,Synapter-method	Synapter
setLowessSpan	Synapter
setLowessSpan,Synapter-method	Synapter
setPepScoreFdr	Synapter
setPepScoreFdr,Synapter-method	Synapter
setPpmError	Synapter
setPpmError,Synapter-method	Synapter
setProtFpr	Synapter
setProtFpr,Synapter-method	Synapter
setQuantPpmError	Synapter
setQuantPpmError,Synapter-method	Synapter
setRtNsd	Synapter
setRtNsd,Synapter-method	Synapter
show,MasterFdrResults-method	MasterFdrResults-class
show,MasterPeptides-method	MasterPeptides-class
show,Synapter-method	Synapter
showFdrStats	Synapter
showFdrStats,Synapter-method	Synapter
Synapter	Synapter
synapter	synapter-package
synapter-defunct	defunct
synapter-deprecated	defunct
synapterGUI	defunct
synapterGuide	synapterGuide
synapterPlgsAgreement	synapterPlgsAgreement
synapterPlgsAgreement,MSnSet-method	synapterPlgsAgreement
synapterTiny	synapterTinyData
synapterTinyData	synapterTinyData
synergise	synergise
synergise1	synergise
synergise2	synergise2
synergize	synergise
synergize1	synergise
synergize2	synergise2
updateObject,Synapter-method	Synapter
validObject,Synapter-method	Synapter
writeFragmentLibrary	makeMaster
writeFragmentLibrary,MasterPeptides,character-method	makeMaster
writeIdentPeptides	Synapter
writeIdentPeptides,Synapter-method	Synapter
writeMasterPeptides	makeMaster
writeMasterPeptides,MasterPeptides,character-method	makeMaster
writeMatchedEMRTs	Synapter
writeMatchedEMRTs,Synapter-method	Synapter
writeMergedPeptides	Synapter
writeMergedPeptides,Synapter-method	Synapter
writeQuantPeptides	Synapter
writeQuantPeptides,Synapter-method	Synapter
