Package: synapter 2.29.0
Laurent Gatto
synapter: Label-free data analysis pipeline for optimal identification and quantitation
The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.
Authors:
synapter_2.29.0.tar.gz
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synapter.pdf |synapter.html✨
synapter/json (API)
| # Install 'synapter' in R: |
| install.packages('synapter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lgatto/synapter/issues
- synapterTiny - Loads a small test data for the 'synapter' package
On BioConductor:synapter-2.29.0(bioc 3.20)synapter-2.28.0(bioc 3.19)
Last updated 2 months agofrom:57f1bcbb5b
Exports:allCombas.MSnSet.SynapterbestCombcreateUniquePeptideDbRdsestimateMasterFdrfileNamesfilterFragmentsfilterIdentPepScorefilterIdentPpmErrorfilterIdentProtFprfilterNonUniqueIdentMatchesfilterNonUniqueMatchesfilterPeptideLengthfilterQuantPepScorefilterQuantPpmErrorfilterQuantProtFprfilterUniqueDbPeptidesfilterUniqueIdentDbPeptidesfilterUniqueMatchesfilterUniqueQuantDbPeptidesfindEMRTsfragmentMatchingfragmentMatchingPerformancegetBestGridParamsgetBestGridValuegetEMRTtablegetFragmentMatchingPpmTolerancegetGridgetGridDetailsgetIdentificationFragmentsgetIdentPpmErrorgetImDiffgetLoggetLowessSpangetPepNumbersgetPepScoreFdrgetPpmErrorQsgetProtFprgetQuantitationSpectragetQuantPpmErrorgetRtNsdgetRtQsinputFilesinspectPeptideScoresmakeMastermasterFdrmergePeptidesmodelIntensitymodelRtperformanceperformance2plotplotCumulativeNumberOfFragmentsplotEMRTtableplotFdrplotFeaturesplotFragmentMatchingplotFragmentMatchingPerformanceplotGridplotIntensityplotPepScoresplotPpmErrorplotRtplotRtDiffsrequantifyrescaleForTop3rescueEMRTssearchGridsetBestGridParamssetFragmentMatchingPpmTolerancesetIdentPpmErrorsetImDiffsetLowessSpansetPepScoreFdrsetPpmErrorsetProtFprsetQuantPpmErrorsetRtNsdshowshowFdrStatsSynaptersynapterGuidesynapterPlgsAgreementsynapterTinyDatasynergisesynergise1synergise2synergizesynergize1synergize2updateObjectwriteFragmentLibrarywriteIdentPeptideswriteMasterPeptideswriteMatchedEMRTswriteMergedPeptideswriteQuantPeptides
Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelBiostringsbitbit64bslibcachemcleaverclicliprclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMSnbaseMultiAssayExperimentmulttestmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesqvalueR6rappdirsRColorBrewerRcppreadrreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomvsnwithrxfunXMLXVectoryamlzlibbioc
Combining HDMSe/MSe data using synapter to optimise identification and quantitation
Rendered fromsynapter.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2018-07-16
Started: 2017-01-16
Fragment matching using synapter
Rendered fromfragmentmatching.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2022-09-27
Started: 2017-01-14
Synapter2 and synergise2
Rendered fromsynapter2.Rmdusingknitr::rmarkdownon Jul 03 2024.Last update: 2018-01-17
Started: 2017-01-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Combine label-free data for optimal identification and quantitation | synapter-package synapter |
| Create an RDS file for the 'Unique Peptides Database' | createUniquePeptideDbRds |
| Computes FDR for all possible final peptide combinations | estimateMasterFdr |
| Inspect peptide scores. | inspectPeptideScores |
| Merges final peptide files | makeMaster writeFragmentLibrary writeFragmentLibrary,MasterPeptides,character-method writeMasterPeptides writeMasterPeptides,MasterPeptides,character-method |
| Class '"MasterFdrResults"' | allComb allComb,MasterFdrResults-method bestComb bestComb,MasterFdrResults-method class:MasterFdrResults fileNames,MasterFdrResults-method masterFdr masterFdr,MasterFdrResults-method MasterFdrResults MasterFdrResults-class plot,MasterFdrResults,missing-method show,MasterFdrResults-method |
| Class '"MasterPeptides"' | class:MasterPeptides MasterPeptides-class show,MasterPeptides-method |
| Plot fragment matching results. | plotFragmentMatching plotFragmentMatching,Synapter-method |
| Intensity requantification | requantify requantify,MSnSet-method |
| Rescale for TOP3 | rescaleForTop3 rescaleForTop3,MSnSet,MSnSet-method |
| Class "Synapter" | as.MSnSet.Synapter class:Synapter dim,Synapter-method filterFragments filterFragments,Synapter-method filterIdentPepScore filterIdentPepScore,Synapter-method filterIdentPpmError filterIdentPpmError,Synapter-method filterIdentProtFpr filterIdentProtFpr,Synapter-method filterNonUniqueIdentMatches filterNonUniqueIdentMatches,Synapter-method filterNonUniqueMatches filterNonUniqueMatches,Synapter-method filterPeptideLength filterPeptideLength,Synapter-method filterQuantPepScore filterQuantPepScore,Synapter-method filterQuantPpmError filterQuantPpmError,Synapter-method filterQuantProtFpr filterQuantProtFpr,Synapter-method filterUniqueDbPeptides filterUniqueDbPeptides,Synapter-method filterUniqueIdentDbPeptides filterUniqueIdentDbPeptides,Synapter-method filterUniqueMatches filterUniqueMatches,Synapter-method filterUniqueQuantDbPeptides filterUniqueQuantDbPeptides,Synapter-method findEMRTs findEMRTs,Synapter-method fragmentMatching fragmentMatching,Synapter-method fragmentMatchingPerformance fragmentMatchingPerformance,Synapter-method getBestGridParams getBestGridParams,Synapter-method getBestGridValue getBestGridValue,Synapter-method getEMRTtable getEMRTtable,Synapter-method getFragmentMatchingPpmTolerance getFragmentMatchingPpmTolerance,Synapter-method getGrid getGrid,Synapter-method getGridDetails getGridDetails,Synapter-method getIdentificationFragments getIdentificationFragments,Synapter-method getIdentPpmError getIdentPpmError,Synapter-method getImDiff getImDiff,Synapter-method getLog getLog,Synapter-method getLowessSpan getLowessSpan,Synapter-method getPepNumbers getPepNumbers,Synapter-method getPepScoreFdr getPepScoreFdr,Synapter-method getPpmErrorQs getPpmErrorQs,Synapter-method getProtFpr getProtFpr,Synapter-method getQuantitationSpectra getQuantitationSpectra,Synapter-method getQuantPpmError getQuantPpmError,Synapter-method getRtNsd getRtNsd,Synapter-method getRtQs getRtQs,Synapter-method inputFiles inputFiles,Synapter-method isCurrent,Synapter-method mergePeptides mergePeptides,Synapter-method modelIntensity modelIntensity,Synapter-method modelRt modelRt,Synapter-method performance performance,Synapter-method performance2 performance2,Synapter-method plotCumulativeNumberOfFragments plotCumulativeNumberOfFragments,Synapter-method plotEMRTtable plotEMRTtable,Synapter-method plotFdr plotFdr,Synapter-method plotFeatures plotFeatures,Synapter-method plotFragmentMatchingPerformance plotFragmentMatchingPerformance,Synapter-method plotGrid plotGrid,Synapter-method plotIntensity plotIntensity,Synapter-method plotPepScores plotPepScores,Synapter-method plotPpmError plotPpmError,Synapter-method plotRt plotRt,Synapter-method plotRtDiffs plotRtDiffs,Synapter-method rescueEMRTs rescueEMRTs,Synapter-method searchGrid searchGrid,Synapter-method setBestGridParams setBestGridParams,Synapter-method setFragmentMatchingPpmTolerance setFragmentMatchingPpmTolerance,Synapter-method setIdentPpmError setIdentPpmError,Synapter-method setImDiff setImDiff,Synapter-method setLowessSpan setLowessSpan,Synapter-method setPepScoreFdr setPepScoreFdr,Synapter-method setPpmError setPpmError,Synapter-method setProtFpr setProtFpr,Synapter-method setQuantPpmError setQuantPpmError,Synapter-method setRtNsd setRtNsd,Synapter-method show,Synapter-method showFdrStats showFdrStats,Synapter-method Synapter updateObject,Synapter-method validObject,Synapter-method writeIdentPeptides writeIdentPeptides,Synapter-method writeMatchedEMRTs writeMatchedEMRTs,Synapter-method writeMergedPeptides writeMergedPeptides,Synapter-method writeQuantPeptides writeQuantPeptides,Synapter-method |
| Opens the 'synapter' vignette | synapterGuide |
| Synapter/PLGS Agreement | synapterPlgsAgreement synapterPlgsAgreement,MSnSet-method |
| Loads a small test data for the 'synapter' package | synapterTiny synapterTinyData |
| Synergise identification and quantitation results | synergise synergise1 synergize synergize1 |
| Synergise identification and quantitation results | synergise2 synergize2 |
