metapone

DOI: 10.18129/B9.bioc.metapone    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see metapone.

Conducts pathway test of metabolomics data using a weighted permutation test

Bioconductor version: 3.15

The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.

Author: Leqi Tian [aut], Tianwei Yu [aut], Tianwei Yu [cre]

Maintainer: Tianwei Yu <yutianwei at cuhk.edu.cn>

Installation

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

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

BiocManager::install("metapone")

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("metapone")

 

HTML	R Script	metapone
PDF		Reference Manual

Details

biocViews	MassSpectrometry, Metabolomics, Pathways, Software, Technology
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	Artistic-2.0
Depends	R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel
Imports	methods
LinkingTo
Suggests	rmarkdown, knitr
SystemRequirements
Enhances
URL
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	metapone_1.2.0.tar.gz
Windows Binary	metapone_1.2.0.zip
macOS Binary (x86_64)	metapone_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metapone
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metapone
Package Short Url	https://bioconductor.org/packages/metapone/
Package Downloads Report	Download Stats