ptairMS

DOI: 10.18129/B9.bioc.ptairMS    

Pre-processing PTR-TOF-MS Data

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	ptaiMS: Processing and analysis of PTR-TOF-MS data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Software
Version	1.2.0
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
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
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls
SystemRequirements
Enhances
URL
BugReports	https://github.com/camilleroquencourt/ptairMS/issues
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_1.2.0.tar.gz
Windows Binary	ptairMS_1.2.0.zip
macOS 10.13 (High Sierra)	ptairMS_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ptairMS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ptairMS
Package Short Url	https://bioconductor.org/packages/ptairMS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive