MsFeatures

This is the development version of MsFeatures; for the stable release version, see MsFeatures.

Functionality for Mass Spectrometry Features

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("MsFeatures")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Software
Version	1.9.0
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
Linking To
Suggests	testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
System Requirements
Enhances
URL	https://github.com/RforMassSpectrometry/MsFeatures
Bug Reports	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_1.9.0.tar.gz
Windows Binary	MsFeatures_1.9.0.zip
macOS Binary (x86_64)	MsFeatures_1.9.0.tgz
macOS Binary (arm64)	MsFeatures_1.9.0.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