ptairMS
Pre-processing PTR-TOF-MS Data
Bioconductor version: Release (3.17)
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 single 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.
Author: camille Roquencourt [aut, cre]
Maintainer: camille Roquencourt <camille.roquencourt at hotmail.fr>
citation("ptairMS")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ptairMS")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ptairMS")| ptaiMS: Processing and analysis of PTR-TOF-MS data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (2 years) |
| License | GPL-3 |
| Depends | |
| 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 |
| Linking To | Rcpp |
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls |
| System Requirements | |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/camilleroquencourt/ptairMS/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ptairMS_1.8.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | ptairMS_1.8.0.tgz |
| macOS Binary (arm64) | ptairMS_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ptairMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ptairMS |
| Bioc Package Browser | https://code.bioconductor.org/browse/ptairMS/ |
| Package Short Url | https://bioconductor.org/packages/ptairMS/ |
| Package Downloads Report | Download Stats |