msmsTests

DOI: 10.18129/B9.bioc.msmsTests    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see msmsTests.

LC-MS/MS Differential Expression Tests

Bioconductor version: 3.11

Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

Author: Josep Gregori, Alex Sanchez, and Josep Villanueva

Maintainer: Josep Gregori i Font <josep.gregori at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("msmsTests")

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("msmsTests")

 

PDF	R Script	msmsTests: controlling batch effects by blocking
PDF	R Script	msmsTests: post test filters to improve reproducibility
PDF		Reference Manual

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.26.0
In Bioconductor since	BioC 2.13 (R-3.0) (7 years)
License	GPL-2
Depends	R (>= 3.0.1), MSnbase, msmsEDA
Imports	edgeR, qvalue
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	MSnID, RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	msmsTests_1.26.0.tar.gz
Windows Binary	msmsTests_1.26.0.zip
macOS 10.13 (High Sierra)	msmsTests_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msmsTests
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msmsTests
Package Short Url	https://bioconductor.org/packages/msmsTests/
Package Downloads Report	Download Stats