PSMatch
Bioc currentHandling and Managing Peptide Spectrum Matches
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
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.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
41 24 exported
Complexity
3.6 avg / 12 max
Call network
41 nodes / 37 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
6,460
Files
51
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
26
Internal functions
16
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.67
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
23.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (5)
Bioconductor (5)
People
- Laurent Gatto author maintainer
- Thomas Burger contributor
- Guillaume Deflandre contributor
- Sebastian Gibb author
- Johannes Rainer author
- Samuel Wieczorek contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("PSMatch")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.