adductomicsR
Bioc currentProcessing of adductomic mass spectral datasets
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
26 10 exported
Complexity
10.5 avg / 41 max
Call network
26 nodes / 16 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
8,635
Files
84
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
11
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
9
Dep constraint coverage
89.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 28
- Examples that run
- 80%8 run in a plain check · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Adductomics workflow HTML
Repository practices
Checks run against github.com/josielhayes/adductomicsr on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ElementMasses | data.frame | 10 × 9 | No other package |
| allResults_ALVLIAFAQYLQQCPFEDHVK_example | data.frame | 96 × 44 | No other package |
| exampleFalsePosTable | data.frame | 1 × 9 | No other package |
| examplePeakTable | data.frame | 131 × 5 | No other package |
| exampleTruePosTable | data.frame | 9 × 9 | No other package |
| example_adductQuantif_peakList | data.frame | 49 × 20 | No other package |
| exampletargTable2 | data.frame | 59 × 4 | No other package |
| internalStd_scansTable | data.frame | 1 × 10 | No other package |
| modelSpectrum_ALVLIAFAQYLQQCPFEDHVK | data.frame | 64 × 4 | No other package |
| modelSpectrum_RHPYFYAPELLFFAK | data.frame | 48 × 4 | No other package |
| runOrder | data.frame | 2 × 2 | No other package |
| runOrder2 | data.frame | 2 × 2 | No other package |
| runOrderR3.5 | data.frame | 7 × 2 | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("adductomicsR")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.