ptairMS
Bioc currentPre-processing PTR-TOF-MS Data
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl<e ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
96 18 exported
Complexity
5.8 avg / 52 max
Call network
96 nodes / 102 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
15,928
Files
92
Compiled share
0.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
31
Internal functions
72
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
90
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-09-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
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
- 53 (16 internal)includes a package overview page
- Examples that run
- 97%31 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 6%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/camilleroquencourt/ptairms on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| HDBD | – | – | – |
| atomic_isotopes | data.frame | 52 × 5 | No other package |
| atomic_weights | data.frame | 87 × 5 | No other package |
| calib_table | data.frame | 6 × 3 | No other package |
| manualAdd | data.frame | 11 × 12 | No other package |
| vocDB | data.frame | 323 × 12 | No other package |
Topics
People
- camille Roquencourt author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ptairMS")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.