MsQuality

DOI: 10.18129/B9.bioc.MsQuality  

MsQuality - Quality metric calculation from Spectra and MsExperiment objects

Bioconductor version: Release (3.17)

The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

Author: Thomas Naake [aut, cre] , Johannes Rainer [aut]

Maintainer: Thomas Naake <thomasnaake at googlemail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MsQuality")

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("MsQuality")

 

HTML	R Script	QC for metabolomics and proteomics data
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Metabolomics, Proteomics, QualityControl, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), MsExperiment(>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics(>= 1.24.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra(>= 1.2.0), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), BiocParallel
LinkingTo
Suggests	BiocGenerics(>= 0.24.0), BiocStyle(>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), msdata(>= 0.32.0), mzR(>= 2.32.0), rmarkdown (>= 2.7), S4Vectors(>= 0.29.17), testthat (>= 2.2.1)
SystemRequirements
Enhances
URL	https://www.github.com/tnaake/MsQuality/
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	MsQuality_1.0.0.tar.gz
Windows Binary	MsQuality_1.0.0.zip
macOS Binary (x86_64)	MsQuality_1.0.0.tgz
macOS Binary (arm64)	MsQuality_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MsQuality
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MsQuality
Bioc Package Browser	https://code.bioconductor.org/browse/MsQuality/
Package Short Url	https://bioconductor.org/packages/MsQuality/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive