synapter-package | Combine label-free data for optimal identification and quantitation |
allComb | Class '"MasterFdrResults"' |
allComb-method | Class '"MasterFdrResults"' |
as.MSnSet.Synapter | Class "Synapter" |
bestComb | Class '"MasterFdrResults"' |
bestComb-method | Class '"MasterFdrResults"' |
class:MasterFdrResults | Class '"MasterFdrResults"' |
class:MasterPeptides | Class '"MasterPeptides"' |
class:Synapter | Class "Synapter" |
dim-method | Class "Synapter" |
estimateMasterFdr | Computes FDR for all possible final peptide combinations |
fileNames-method | Class '"MasterFdrResults"' |
filterIdentPepScore | Class "Synapter" |
filterIdentPepScore-method | Class "Synapter" |
filterIdentPpmError | Class "Synapter" |
filterIdentPpmError-method | Class "Synapter" |
filterIdentProtFpr | Class "Synapter" |
filterIdentProtFpr-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" |
filterUniqueQuantDbPeptides | Class "Synapter" |
filterUniqueQuantDbPeptides-method | Class "Synapter" |
findEMRTs | Class "Synapter" |
findEMRTs-method | Class "Synapter" |
getBestGridParams | Class "Synapter" |
getBestGridParams-method | Class "Synapter" |
getBestGridValue | Class "Synapter" |
getBestGridValue-method | Class "Synapter" |
getEMRTtable | Class "Synapter" |
getEMRTtable-method | Class "Synapter" |
getGrid | Class "Synapter" |
getGrid-method | Class "Synapter" |
getGridDetails | Class "Synapter" |
getGridDetails-method | Class "Synapter" |
getIdentPpmError | Class "Synapter" |
getIdentPpmError-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" |
getQuantPpmError | Class "Synapter" |
getQuantPpmError-method | Class "Synapter" |
getRtNsd | Class "Synapter" |
getRtNsd-method | Class "Synapter" |
getRtQs | Class "Synapter" |
getRtQs-method | Class "Synapter" |
inputFiles | Class "Synapter" |
inputFiles-method | Class "Synapter" |
inspectPeptideScores | Inspect peptide scores. |
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" |
modelRt | Class "Synapter" |
modelRt-method | Class "Synapter" |
performance | Class "Synapter" |
performance-method | Class "Synapter" |
performance2 | Class "Synapter" |
performance2-method | Class "Synapter" |
plot-method | Class '"MasterFdrResults"' |
plotEMRTtable | Class "Synapter" |
plotEMRTtable-method | Class "Synapter" |
plotFdr | Class "Synapter" |
plotFdr-method | Class "Synapter" |
plotFeatures | Class "Synapter" |
plotFeatures-method | Class "Synapter" |
plotGrid | Class "Synapter" |
plotGrid-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" |
searchGrid | Class "Synapter" |
searchGrid-method | Class "Synapter" |
setBestGridParams | Class "Synapter" |
setBestGridParams-method | Class "Synapter" |
setIdentPpmError | Class "Synapter" |
setIdentPpmError-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 |
synapterGUI | Launch the synapter GUI |
synapterGuide | Opens the 'synapter' vignette |
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 |
synergize | Synergise identification and quantitation results |
writeIdentPeptides | Class "Synapter" |
writeIdentPeptides-method | Class "Synapter" |
writeMasterPeptides | 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" |