MsFeatures

DOI: 10.18129/B9.bioc.MsFeatures  

Functionality for Mass Spectrometry Features

Bioconductor version: Release (3.16)

The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.

Author: Johannes Rainer [aut, cre]

Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("MsFeatures")

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("MsFeatures")

 

HTML	R Script	Grouping Mass Spectrometry Features
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Software
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	Artistic-2.0
Depends	R (>= 4.1)
Imports	methods, ProtGenerics(>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats
LinkingTo
Suggests	testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/RforMassSpectrometry/MsFeatures
BugReports	https://github.com/RforMassSpectrometry/MsFeatures/issues
Depends On Me
Imports Me	xcms
Suggests Me	qmtools
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MsFeatures_1.6.0.tar.gz
Windows Binary	MsFeatures_1.6.0.zip
macOS Binary (x86_64)	MsFeatures_1.6.0.tgz
macOS Binary (arm64)	MsFeatures_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MsFeatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MsFeatures
Bioc Package Browser	https://code.bioconductor.org/browse/MsFeatures/
Package Short Url	https://bioconductor.org/packages/MsFeatures/
Package Downloads Report	Download Stats