API for synapter
Label-free data analysis pipeline for optimal identification and quantitation

Global functions
MasterFdrResults Man page
MasterFdrResults-class Man page
MasterPeptides-class Man page
Synapter Man page Source code
allComb Man page
allComb,MasterFdrResults-method Man page
appendFragmentMatchingColumn Source code
as.MSnSet.Synapter Man page Source code
bestComb Man page
bestComb,MasterFdrResults-method Man page
calculateGridPerformance Source code
calculatePeptideFileCombinations Source code
catIsotopeDistr Source code
class:MasterFdrResults Man page
class:MasterPeptides Man page
class:Synapter Man page
commonColnames Source code
correctIntensity Source code
createEmptyMsnbaseSpectrum2 Source code
createFragmentLibrary Source code
createMs2SpectrumFromFragments Source code
createMs2SpectrumFromSpectrumXml Source code
createMsnbaseSpectrum2 Source code
createUniquePeptideDbRds Man page Source code
cumsumIntensities Source code
dbUniquePeptideSet Source code Source code
diagnosticErrors Source code
dim,Synapter-method Man page
doHDMSePredictions Source code
duplicated2 Source code
error.ppm Source code
estimate.mass.range Source code
estimateMasterFdr Man page Source code
fileNames,MasterFdrResults-method Man page
filter.error.ppm Source code
filterDuplicatedPeptideSequences Source code
filterEmptyFragments Source code
filterFragments Man page
filterFragments,Synapter-method Man page
filterFunction Source code
filterIdentPepScore Man page
filterIdentPepScore,Synapter-method Man page
filterIdentPpmError Man page
filterIdentPpmError,Synapter-method Man page
filterIdentProtFpr Man page
filterIdentProtFpr,Synapter-method Man page
filterIntensity Source code
filterMissingRuns Source code
filterNeutralLoss Source code
filterNonUniqueIdentMatches Man page Source code
filterNonUniqueIdentMatches,Synapter-method Man page
filterNonUniqueMatches Man page Source code
filterNonUniqueMatches,Synapter-method Man page
filterPepScore Source code
filterPeptideLength Man page
filterPeptideLength,Synapter-method Man page
filterPeptideMatchType Source code
filterProtFpr Source code
filterQuantPepScore Man page
filterQuantPepScore,Synapter-method Man page
filterQuantPpmError Man page
filterQuantPpmError,Synapter-method Man page
filterQuantProtFpr Man page
filterQuantProtFpr,Synapter-method Man page
filterUniqueDbPeptides Man page
filterUniqueDbPeptides,Synapter-method Man page
filterUniqueIdentDbPeptides Man page
filterUniqueIdentDbPeptides,Synapter-method Man page
filterUniqueMatches Man page Source code
filterUniqueMatches,Synapter-method Man page
filterUniqueQuantDbPeptides Man page
filterUniqueQuantDbPeptides,Synapter-method Man page
finalFragment2spectra Source code
findEMRTs Man page
findEMRTs,Synapter-method Man page
findImIndices Source code
findMSeEMRTs Source code
findMzIndices Source code
findRtIndices Source code
findSynapterPlgsAgreement Source code
flatMatchedEMRTs Source code
fragmentMatching Man page Source code
fragmentMatching,Synapter-method Man page
fragmentMatchingConfusionMatrix Source code
fragmentMatchingContingencyMatrix Source code
fragmentMatchingDifferences Source code
fragmentMatchingPerformance Man page
fragmentMatchingPerformance,Synapter-method Man page
fragments2spectra Source code
getBestGridParams Man page
getBestGridParams,Synapter-method Man page
getBestGridValue Man page
getBestGridValue,Synapter-method Man page
getEMRTtable Man page
getEMRTtable,Synapter-method Man page
getFragmentMatchingPpmTolerance Man page
getFragmentMatchingPpmTolerance,Synapter-method Man page
getFragmentStrFromFragments Source code
getGrid Man page
getGrid,Synapter-method Man page
getGridDetails Man page
getGridDetails,Synapter-method Man page
getIdStats Source code
getIdentPpmError Man page
getIdentPpmError,Synapter-method Man page
getIdentificationFragments Man page
getIdentificationFragments,Synapter-method Man page
getImDiff Man page
getImDiff,Synapter-method Man page
getLog Man page
getLog,Synapter-method Man page
getLowessSpan Man page
getLowessSpan,Synapter-method Man page
getPepNumbers Man page
getPepNumbers,Synapter-method Man page
getPepScoreFdr Man page
getPepScoreFdr,Synapter-method Man page
getPeptideSeqFromFragments Source code
getPpmErrorQs Man page
getPpmErrorQs,Synapter-method Man page
getProtFpr Man page
getProtFpr,Synapter-method Man page
getQs Source code
getQuantPpmError Man page
getQuantPpmError,Synapter-method Man page
getQuantitationSpectra Man page
getQuantitationSpectra,Synapter-method Man page
getRtNsd Man page
getRtNsd,Synapter-method Man page
getRtQs Man page
getRtQs,Synapter-method Man page
getSpectrum Source code
gridSearch3 Source code
inputFiles Man page
inputFiles,Synapter-method Man page
inspectPeptideScores Man page Source code
isCorrespondingPep3DataFile Source code
isCurrent,Synapter-method Man page
keepUniqueSpectrumIds Source code
loadIdentOnly Source code
loessModel Source code
loessModelPredSd Source code
makeFigurePath Source code
makeMaster Man page Source code
masterFdr Man page
masterFdr,MasterFdrResults-method Man page
masterFdrSummary Source code
matched.quant.spectrumIDs2numeric Source code
mergeMaster Source code
mergePeptideData Source code
mergePeptides Man page
mergePeptides,Synapter-method Man page
modelIntensity Man page Source code
modelIntensity,Synapter-method Man page
modelRetTime Source code
modelRt Man page
modelRt,Synapter-method Man page
names2chargesIsotopes Source code
onAttach Source code
orderForMasterModels Source code
peptideMatrix Source code
performance Man page
performance,Synapter-method Man page
performance2 Man page
performance2,Synapter-method Man page
plot,MasterFdrResults,missing-method Man page
plot.all.features Source code
plot.some.features Source code
plotCumulativeNumberOfFragments Man page
plotCumulativeNumberOfFragments,Synapter-method Man page
plotCxRow Source code
plotEMRTtable Man page
plotEMRTtable,Synapter-method Man page
plotErrorPpm Source code
plotFdr Man page
plotFdr,Synapter-method Man page
plotFeatures Man page
plotFeatures,Synapter-method Man page
plotFragmentMatching Man page Source code
plotFragmentMatching,Synapter-method Man page
plotFragmentMatchingPerformance Man page Source code
plotFragmentMatchingPerformance,Synapter-method Man page
plotFragmentsVsSpectrum Source code
plotGrid Man page
plotGrid,Synapter-method Man page
plotIntensity Man page
plotIntensity,Synapter-method Man page
plotIntensityVsNumber Source code
plotLowessData Source code
plotLowessModel Source code
plotPepScores Man page
plotPepScores,Synapter-method Man page
plotPpmError Man page
plotPpmError,Synapter-method Man page
plotRetTimeDiffs Source code
plotRt Man page
plotRt,Synapter-method Man page
plotRtDiffs Man page
plotRtDiffs,Synapter-method Man page
plotSpectrumVsSpectrum Source code
predictIntensities Source code
qPlot Source code
readFinalPeptides Source code
readFragments Source code
readPep3D Source code
readSynapterSpectrumXml Source code
readcsv Source code
recalculateFragmentIntensities Source code
referenceRun Source code
regeneratePrecursorLeId Source code
requantify Man page Source code
requantify,MSnSet-method Man page
requantifyReferenceRun Source code
requantifySum Source code
requantifyTheoreticalDistribution Source code
rescaleForTop3 Man page Source code
rescaleForTop3,MSnSet,MSnSet-method Man page
rescueEMRTs Man page Source code
rescueEMRTs,Synapter-method Man page
runsUnsaturated Source code
sCommonIsotope Source code
sCurrent Source code
sUnsaturatedIsotope Source code
score2pval Source code
searchGrid Man page
searchGrid,Synapter-method Man page
setBestGridParams Man page
setBestGridParams,Synapter-method Man page
setFragmentMatchingPpmTolerance Man page
setFragmentMatchingPpmTolerance,Synapter-method Man page
setIdentPpmError Man page
setIdentPpmError,Synapter-method Man page
setImDiff Man page
setImDiff,Synapter-method Man page
setLowessSpan Man page
setLowessSpan,Synapter-method Man page
setPepScoreFdr Man page
setPepScoreFdr,Synapter-method Man page
setPpmError Man page
setPpmError,Synapter-method Man page
setProtFpr Man page
setProtFpr,Synapter-method Man page
setQuantPpmError Man page
setQuantPpmError,Synapter-method Man page
setRtNsd Man page
setRtNsd,Synapter-method Man page
show,MasterFdrResults-method Man page
show,MasterPeptides-method Man page
show,Synapter-method Man page
showFdrStats Man page
showFdrStats,Synapter-method Man page
sotopicDistr2matrix Source code
spectrumXml2spectra Source code
sumAllPeakCounts Source code
synapter Man page
synapter-defunct Man page
synapter-deprecated Man page
synapter-package Man page
synapterGUI Man page Source code
synapterGuide Man page Source code
synapterPlgsAgreement Man page Source code
synapterPlgsAgreement,MSnSet-method Man page
synapterTiny Man page
synapterTinyData Man page Source code
synergise Man page Source code
synergise1 Man page
synergise2 Man page
synergize Man page
synergize1 Man page
synergize2 Man page
table Source code
updateObject,Synapter-method Man page
updateSynapterObject Source code
validObject,Synapter-method Man page
validSynapterObject Source code
writeFragmentLibrary Man page
writeFragmentLibrary,MasterPeptides,character-method Man page
writeIdentPeptides Man page
writeIdentPeptides,Synapter-method Man page
writeMasterPeptides Man page
writeMasterPeptides,MasterPeptides,character-method Man page
writeMatchedEMRTs Man page
writeMatchedEMRTs,Synapter-method Man page
writeMergedPeptides Man page
writeMergedPeptides,Synapter-method Man page
writeQuantPeptides Man page
writeQuantPeptides,Synapter-method Man page
synapter documentation built on May 31, 2017, 3:47 p.m.