Package: ptairMS
Title: Pre-processing PTR-TOF-MS Data
Version: 1.21.0
Date: 2020-03-18
Authors@R: person("camille", "Roquencourt", email = "camille.roquencourt@hotmail.fr", role = c("aut", "cre"))
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.
License: GPL-3
Encoding: UTF-8
BugReports: https://github.com/camilleroquencourt/ptairMS/issues
RoxygenNote: 7.2.3
Imports: Biobase, bit64, chron, data.table, doParallel, DT, enviPat,
        foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra,
        Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5,
        rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats,
        utils
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
        ropls
VignetteBuilder: knitr
LinkingTo: Rcpp
NeedsCompilation: yes
biocViews: Software, MassSpectrometry, Preprocessing, Metabolomics,
        PeakDetection, Alignment
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:55:37 UTC
RemoteUrl: https://github.com/bioc/ptairMS
RemoteRef: HEAD
RemoteSha: 258decba3c9deb98696635441ba25eb7a6b8b051
Packaged: 2026-07-04 22:47:58 UTC; root
Author: camille Roquencourt [aut, cre]
Maintainer: camille Roquencourt <camille.roquencourt@hotmail.fr>