MassSpecWavelet
Bioc currentPeak Detection for Mass Spectrometry data using wavelet-based algorithms
Release Lineage
Entered 2.0 · Apr 26, 2007
Current · Requires R 4.6
Description
Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
41 13 exported
Complexity
6.4 avg / 24 max
Call network
41 nodes / 38 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
4,251
Files
60
Compiled share
12.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
13
Internal functions
14
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
LGPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
39
First release
2007-04-24
Latest release
2026-07-06
Avg cadence
184 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22 (2 internal)includes a package overview page
- Examples that run
- 88%14 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 93%
- Return-value docs
- 100%
- Help pages citing references
- 23%
tuneInPeakInfo(): Fix three crashes found while adding unit tests for this function:- A peak whose local refinement window contains no ridges (e.g. a quiet/flat neighborhood) crashed with
Error in strsplit(ridgeName.i, "_") : non-character argument(the same bug class fixed earlier inidentifyMajorPeaks()). That peak is now left unprocessed instead. - Calling
tuneInPeakInfo()via the directpeakIndex/peakScalearguments (instead ofmajorPeakInfo) could crash withattempt to set an attribute on NULLif any peak ended up unprocessed.NAis now used as a placeholder when there is no original value to fall back on.
Show all changes in 1.78.2Hide the rest of the changes in 1.78.2
peakDetectionCWT(tuneIn = TRUE)on a flat/constant signal (whosemajorPeakInfo$peakIndexis empty) crashed withmissing value where TRUE/FALSE needed, sincefor (i in 1:length(x))iterates twice whenxhas length 0. Fixed to return a well-formed empty result instead.
From NEWS.md in the release
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/zeehio/massspecwavelet on 2026-10-22.
The repository owner accepts GitHub Sponsors
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| exampleMS | matrix | 37,656 × 1 | No other package |
Topics
Depended on by (5)
CRAN (3)
Suggested by (4)
People
- Sergio Oller Moreno author maintainer
- Pan Du author
- Warren Kibbe author
- Simon Lin author
Cite
Cite this package
Run in R for the authors' entry:
citation("MassSpecWavelet")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btl355.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.