globaltest

DOI: 10.18129/B9.bioc.globaltest    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see globaltest.

Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing

Bioconductor version: 3.8

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Author: Jelle Goeman and Jan Oosting, with contributions by Livio Finos and Aldo Solari

Maintainer: Jelle Goeman <j.j.goeman at lumc.nl>

Installation

To install this package, start R (version "3.5") and enter:

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

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("globaltest")

 

PDF	R Script	Global Test
PDF		Reference Manual

Details

biocViews	Bioinformatics, DifferentialExpression, GO, Microarray, OneChannel, Pathways, Software
Version	5.36.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14 years)
License	GPL (>= 2)
Depends	methods, survival
Imports	Biobase, AnnotationDbi, annotate, graphics
LinkingTo
Suggests	vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart
SystemRequirements
Enhances
URL
Depends On Me	GlobalAncova
Imports Me	BiSeq, ChAMP, EGSEA, SIM
Suggests Me	topGO
Links To Me
Build Report

Package Archives

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

Source Package	globaltest_5.36.0.tar.gz
Windows Binary	globaltest_5.36.0.zip
Mac OS X 10.11 (El Capitan)	globaltest_5.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/globaltest
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/globaltest
Package Short Url	http://bioconductor.org/packages/globaltest/
Package Downloads Report	Download Stats