Package: PSMatch 1.11.2

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_1.11.2.tar.gz
PSMatch_1.11.2.zip(r-4.5)PSMatch_1.11.2.zip(r-4.4)PSMatch_1.11.2.zip(r-4.3)
PSMatch_1.11.2.tgz(r-4.5-any)PSMatch_1.11.2.tgz(r-4.4-any)PSMatch_1.11.2.tgz(r-4.3-any)
PSMatch_1.11.2.tar.gz(r-4.5-noble)PSMatch_1.11.2.tar.gz(r-4.4-noble)
PSMatch_1.11.2.tgz(r-4.4-emscripten)PSMatch_1.11.2.tgz(r-4.3-emscripten)
PSMatch.pdf |PSMatch.html
PSMatch/json (API)
NEWS

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

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

On BioConductor:PSMatch-1.11.0(bioc 3.21)PSMatch-1.10.0(bioc 3.20)

infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches

8.20 score 3 stars 39 packages 15 scripts 30 exports 106 dependencies

Last updated 2 months agofrom:5dc7a07f8b. Checks:4 OK, 3 NOTE, 2 ERROR. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKApr 02 2025
R-4.5-winNOTEApr 02 2025
R-4.5-macNOTEApr 02 2025
R-4.5-linuxNOTEApr 02 2025
R-4.4-winOKApr 02 2025
R-4.4-macOKApr 02 2025
R-4.4-linuxOKApr 02 2025
R-4.3-winERRORApr 02 2025
R-4.3-macERRORApr 02 2025

Exports:addFragmentsadjacencyMatrixcalculateFragmentsccMatrixconnectedComponentsConnectedComponentsdefaultNeutralLossdescribePeptidesdescribeProteinsdimsfilterPsmDecoyfilterPsmFdrfilterPsmRankfilterPSMsfilterPsmSharedgetAminoAcidsgetAtomicMassmakeAdjacencyMatrixmakePeptideProteinVectorncolsnrowsplotAdjacencyMatrixprioritiseConnectedComponentsprioritizeConnectedComponentsPSMpsmVariablesreadPSMsreducedreduced<-reducePSMs

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryaml

MS2 fragment ions

Rendered fromFragments.Rmdusingknitr::rmarkdownon Apr 02 2025.

Last update: 2022-02-14
Started: 2022-02-14

Understanding protein groups with adjacency matrices

Rendered fromAdjacencyMatrix.Rmdusingknitr::rmarkdownon Apr 02 2025.

Last update: 2023-04-03
Started: 2022-02-09

Working with PSM data

Rendered fromPSM.Rmdusingknitr::rmarkdownon Apr 02 2025.

Last update: 2022-03-20
Started: 2020-10-28

Readme and manuals

Help Manual

Help pageTopics
Adds MS2 FragmentsaddFragments
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
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