Package: PSMatch 1.11.0
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:
PSMatch_1.11.0.tar.gz
PSMatch_1.11.0.zip(r-4.5)PSMatch_1.11.0.zip(r-4.4)PSMatch_1.11.0.zip(r-4.3)
PSMatch_1.11.0.tgz(r-4.4-any)PSMatch_1.11.0.tgz(r-4.3-any)
PSMatch_1.11.0.tar.gz(r-4.5-noble)PSMatch_1.11.0.tar.gz(r-4.4-noble)
PSMatch_1.11.0.tgz(r-4.4-emscripten)PSMatch_1.11.0.tgz(r-4.3-emscripten)
PSMatch.pdf |PSMatch.html✨
PSMatch/json (API)
NEWS
| # 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-1.11.0(bioc 3.21)PSMatch-1.10.0(bioc 3.20)
infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches
Last updated 23 days agofrom:e8f78a1851. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:addFragmentsadjacencyMatrixcalculateFragmentsccMatrixconnectedComponentsConnectedComponentsdefaultNeutralLossdescribePeptidesdescribeProteinsdimsfilterPsmDecoyfilterPsmFdrfilterPsmRankfilterPSMsfilterPsmSharedgetAminoAcidsgetAtomicMassmakeAdjacencyMatrixmakePeptideProteinVectorncolsnrowsplotAdjacencyMatrixprioritiseConnectedComponentsprioritizeConnectedComponentsPSMpsmVariablesreadPSMsreducedreduced<-reducePSMs
Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplotlyplyrpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc
MS2 fragment ions
Rendered fromFragments.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2022-02-14
Started: 2022-02-14
Understanding protein groups with adjacency matrices
Rendered fromAdjacencyMatrix.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-04-03
Started: 2022-02-09
Working with PSM data
Rendered fromPSM.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2022-03-20
Started: 2020-10-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adds MS2 Fragments | addFragments |
| Convert to/from an adjacency matrix. | adjacencyMatrix makeAdjacencyMatrix makePeptideProteinVector plotAdjacencyMatrix |
| Calculate ions produced by fragmentation | calculateFragments calculateFragments,character,missing-method defaultNeutralLoss |
| Connected components | adjacencyMatrix,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 compositions | describePeptides describeProteins |
| Filter out unreliable PSMs. | filterPsmDecoy filterPsmFdr filterPsmRank filterPSMs filterPsmShared |
| Amino acids | getAminoAcids |
| Atomic mass. | getAtomicMass |
| A class for peptide-spectrum matches | adjacencyMatrix,PSM-method PSM PSM,character PSM,data.frame PSM,PSM PSM-class psmVariables readPSMs reduced reduced<- reducePSMs |
| PSMatch: Handling and Managing Peptide Spectrum Matches | PSMatch-package PSMatch |
