Package: PSMatch 1.17.0

Laurent Gatto

PSMatch: Handling and Managing Peptide Spectrum Matches

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

Authors:Laurent Gatto [aut, cre], Johannes Rainer [aut], Sebastian Gibb [aut], Samuel Wieczorek [ctb], Thomas Burger [ctb], Guillaume Deflandre [ctb]

PSMatch_1.17.0.tar.gz
PSMatch_1.17.0.zip(r-4.7-any)PSMatch_1.17.0.zip(r-4.6-any)PSMatch_1.17.0.zip(r-4.5-any)
PSMatch_1.17.0.tgz(r-4.6-any)PSMatch_1.17.0.tgz(r-4.5-any)
PSMatch_1.17.0.tar.gz(r-4.7-any)PSMatch_1.17.0.tar.gz(r-4.6-any)
PSMatch_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PSMatch/json (API)

# Install 'PSMatch' in R:
install.packages('PSMatch', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/psm/issues

On BioConductor:PSMatch-1.17.0(bioc 3.24)PSMatch-1.16.0(bioc 3.23)

infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches

8.50 score 7 stars 48 packages 64 scripts 4.9k downloads 31 exports 103 dependencies

Last updated from:3ec4d55b28. Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: yes.

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bioc-checksNOTE208
linux-develERROR404
source / vignettesERROR471
linux-releaseERROR385
macos-releaseERROR264
macos-oldrelERROR250
windows-develERROR284
windows-releaseERROR321
windows-oldrelERROR277
wasm-releaseOK176

Exports:adjacencyMatrixcalculateFragmentsccMatrixconnectedComponentsConnectedComponentsdefaultNeutralLossdescribePeptidesdescribeProteinsdimsfilterPsmDecoyfilterPsmFdrfilterPsmRankfilterPSMsfilterPsmSharedgetAminoAcidsgetAtomicMasslabelFragmentsmakeAdjacencyMatrixmakePeptideProteinVectorncolsnrowsplotAdjacencyMatrixplotSpectraPTMprioritiseConnectedComponentsprioritizeConnectedComponentsPSMpsmVariablesreadPSMsreducedreduced<-reducePSMs

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericsPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Convert to/from an adjacency matrix.adjacencyMatrix makeAdjacencyMatrix makePeptideProteinVector plotAdjacencyMatrix
Calculate ions produced by fragmentation with variable modificationscalculateFragments calculateFragments,character,missing-method defaultNeutralLoss modificationPositions
Connected componentsadjacencyMatrix,ConnectedComponents adjacencyMatrix,ConnectedComponents-method ccMatrix ConnectedComponents connectedComponents ConnectedComponents-class dims,ConnectedComponents dims,ConnectedComponents-method length,ConnectedComponents length,ConnectedComponents-method ncols,ConnectedComponents ncols,ConnectedComponents-method nrows,ConnectedComponents nrows,ConnectedComponents-method prioritiseConnectedComponents prioritizeConnectedComponents show,ConnectedComponents [,ConnectedComponents,integer,ANY,ANY [,ConnectedComponents,integer,ANY,ANY-method [,ConnectedComponents,logical,ANY,ANY [,ConnectedComponents,logical,ANY,ANY-method [,ConnectedComponents,numeric,ANY,ANY [,ConnectedComponents,numeric,ANY,ANY-method
Describe protein and peptide compositionsdescribePeptides describeProteins
Filter out unreliable PSMs.filterPsmDecoy filterPsmFdr filterPsmRank filterPSMs filterPsmShared
Amino acidsgetAminoAcids
Atomic mass.getAtomicMass
labels MS2 FragmentslabelFragments
Function to plot MS/MS spectra with PTMsplotSpectraPTM
A class for peptide-spectrum matchesadjacencyMatrix,PSM-method PSM PSM,character PSM,data.frame PSM,PSM PSM-class psmVariables readPSMs reduced reduced<- reducePSMs
PSMatch: Handling and Managing Peptide Spectrum MatchesPSMatch-package PSMatch