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

Global functions
.appendFragmentMatchingColumn Source code
.applyByChargeState Source code
.calculatePeptideFileCombinations Source code
.catIsotopeDistr Source code
.commonColnames Source code
.correctIntensity Source code
.createEmptyMsnbaseSpectrum2 Source code
.createFragmentLibrary Source code
.createMs2SpectrumFromFragments Source code
.createMs2SpectrumFromSpectrumXml Source code
.createMsnbaseSpectrum2 Source code
.cumsumIntensities Source code
.dbUniquePeptideSet Source code
.duplicated2 Source code
.filterDuplicatedPeptideSequences Source code
.filterEmptyFragments Source code
.filterIntensity Source code
.filterMissingRuns Source code
.filterNeutralLoss Source code
.filterNonUniqueIdentMatches Source code
.filterNonUniqueMatches Source code
.filterUniqueMatches Source code
.finalFragment2spectra Source code
.findSynapterPlgsAgreement Source code
.fragmentMatching Source code
.fragmentMatchingConfusionMatrix Source code
.fragmentMatchingContingencyMatrix Source code
.fragmentMatchingDifferences Source code
.fragments2spectra Source code
.getFragmentStrFromFragments Source code
.getPeptideSeqFromFragments Source code
.getSpectrum Source code
.isCommonIsotope Source code
.isCurrent Source code
.isUnsaturatedIsotope Source code
.isotopicDistr2matrix Source code
.masterFdrSummary Source code
.mergeMaster Source code
.mergePeptideData Source code
.modelIntensity Source code
.names2chargesIsotopes Source code
.onAttach Source code
.orderForMasterModels Source code
.peptideMatrix Source code
.plotCxRow Source code
.plotFragmentMatching Source code
.plotFragmentMatchingPerformance Source code
.plotFragmentsVsSpectrum Source code
.plotIntensityVsNumber Source code
.plotSpectrumVsSpectrum Source code
.readFragments Source code
.readSynapterSpectrumXml Source code
.recalculateFragmentIntensities Source code
.referenceRun Source code
.regeneratePrecursorLeId Source code
.requantify Source code
.requantifyReferenceRun Source code
.requantifySum Source code
.requantifyTheoreticalDistribution Source code
.rescaleForTop3 Source code
.rescueEMRTs Source code
.runsUnsaturated Source code
.spectrumXml2spectra Source code
.sumAllPeakCounts Source code
.synapterPlgsAgreement Source code
.synergise Source code
.table Source code
.updateSynapterObject Source code
.validSynapterObject Source code
MasterFdrResults Man page
MasterFdrResults-class Man page
MasterPeptides-class Man page
Synapter Man page Source code
allComb Man page
allComb,MasterFdrResults-method Man page
as.MSnSet.Synapter Man page Source code
bestComb Man page
bestComb,MasterFdrResults-method Man page
calculateGridPerformance Source code
class:MasterFdrResults Man page
class:MasterPeptides Man page
class:Synapter Man page
createUniquePeptideDbRds Man page Source code
dbUniquePeptideSet Source code
diagnosticErrors Source code
dim,Synapter-method Man page
doHDMSePredictions 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
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
filterNonUniqueIdentMatches Man page
filterNonUniqueIdentMatches,Synapter-method Man page
filterNonUniqueMatches Man page
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
filterUniqueMatches,Synapter-method Man page
filterUniqueQuantDbPeptides Man page
filterUniqueQuantDbPeptides,Synapter-method Man page
findEMRTs Man page
findEMRTs,Synapter-method Man page
findImIndices Source code
findMSeEMRTs Source code
findMzIndices Source code
findRtIndices Source code
flatMatchedEMRTs Source code
fragmentMatching Man page
fragmentMatching,Synapter-method Man page
fragmentMatchingPerformance Man page
fragmentMatchingPerformance,Synapter-method Man page
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
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
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
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
matched.quant.spectrumIDs2numeric Source code
mergePeptides Man page
mergePeptides,Synapter-method Man page
modelIntensity Man page
modelIntensity,Synapter-method Man page
modelRetTime Source code
modelRt Man page
modelRt,Synapter-method Man page
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
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
plotFragmentMatching,Synapter-method Man page
plotFragmentMatchingPerformance Man page
plotFragmentMatchingPerformance,Synapter-method Man page
plotGrid Man page
plotGrid,Synapter-method Man page
plotIntensity Man page
plotIntensity,Synapter-method Man page
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
predictIntensities Source code
qPlot Source code
readFinalPeptides Source code
readPep3D Source code
readcsv Source code
requantify Man page
requantify,MSnSet-method Man page
rescaleForTop3 Man page
rescaleForTop3,MSnSet,MSnSet-method Man page
rescueEMRTs Man page
rescueEMRTs,Synapter-method Man page
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
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
synapterPlgsAgreement,MSnSet-method Man page
synapterTiny Man page
synapterTinyData Man page Source code
synergise Man page
synergise1 Man page
synergise2 Man page
synergize Man page
synergize1 Man page Source code
synergize2 Man page Source code
updateObject,Synapter-method Man page
validObject,Synapter-method Man page
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
lgatto/synapter documentation built on May 21, 2019, 6:07 a.m.