MsFeatures

DOI: 10.18129/B9.bioc.MsFeatures    

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

Functionality for Mass Spectrometry Features

Bioconductor version: Development (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Software
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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
Links To Me
Build Report  

Package Archives

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

Source Package MsFeatures_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) MsFeatures_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MsFeatures
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MsFeatures
Package Short Url https://bioconductor.org/packages/MsFeatures/
Package Downloads Report Download Stats

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