Package: PSMatch 1.7.2

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]

PSMatch_1.7.2.tar.gz
PSMatch_1.7.2.zip(r-4.5)PSMatch_1.7.2.zip(r-4.4)PSMatch_1.7.2.zip(r-4.3)
PSMatch_1.7.2.tgz(r-4.4-any)PSMatch_1.7.2.tgz(r-4.3-any)
PSMatch_1.7.2.tar.gz(r-4.5-noble)PSMatch_1.7.2.tar.gz(r-4.4-noble)
PSMatch_1.7.2.tgz(r-4.4-emscripten)PSMatch_1.7.2.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-1.9.0(bioc 3.20)PSMatch-1.8.0(bioc 3.19)

infrastructure proteomics massspectrometry mass-spectrometry peptide-spectrum-matches

30 exports 3 stars 4.28 score 107 dependencies 34 dependents 15 scripts

Last updated 6 months agofrom:dddc179844. Checks:OK: 4 NOTE: 2 ERROR: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Sep 15 2024
R-4.5-win	NOTE	Sep 15 2024
R-4.5-linux	NOTE	Sep 15 2024
R-4.4-win	OK	Sep 15 2024
R-4.4-mac	OK	Sep 15 2024
R-4.3-win	OK	Sep 15 2024
R-4.3-mac	ERROR	Sep 15 2024

Exports:addFragments adjacencyMatrix calculateFragments ccMatrix connectedComponents ConnectedComponents defaultNeutralLoss describePeptides describeProteins dims filterPsmDecoy filterPsmFdr filterPsmRank filterPSMs filterPsmShared getAminoAcids getAtomicMass makeAdjacencyMatrix makePeptideProteinVector ncols nrows plotAdjacencyMatrix prioritiseConnectedComponents prioritizeConnectedComponents PSM psmVariables readPSMs reduced reduced<-reducePSMs

Dependencies:abind AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel bslib cachem cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MsCoreUtils MultiAssayExperiment munsell nlme openssl pillar pkgconfig plotly plyr promises ProtGenerics purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

MS2 fragment ions

Rendered fromFragments.Rmdusingknitr::rmarkdownon Sep 15 2024.

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

Understanding protein groups with adjacency matrices

Rendered fromAdjacencyMatrix.Rmdusingknitr::rmarkdownon Sep 15 2024.

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

Working with PSM data

Rendered fromPSM.Rmdusingknitr::rmarkdownon Sep 15 2024.

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

Citation

Development and contributors

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