globaltest

Testing groups of covariates/features for association with a response variable, with applications to gene set testing

Bioconductor version: 2.9

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("globaltest")

To cite this package in a publication, start R and enter:

    citation("globaltest")

Documentation

PDF	R Script	Global Test
PDF	R Script	Global Test (deprecated version 4)
PDF		Reference Manual

Details

biocViews	Microarray, OneChannel, Bioinformatics, DifferentialExpression, GO, Pathways
Depends	methods
Imports	Biobase(>= 2.5.5), survival, AnnotationDbi, annotate, multtest, graphics
Suggests	vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase(>= 2.5.5), survival, GSEABase, penalized, gss, MASS, boot, rpart
System Requirements
License	GPL (>= 2)
URL	http://www.msbi.nl/goeman
Depends On Me	GlobalAncova
Imports Me	SIM
Suggests Me	topGO
Version	5.8.1
Since	Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source	globaltest_5.8.1.tar.gz
Windows Binary	globaltest_5.8.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	globaltest_5.8.1.tgz
Package Downloads Report	Download Stats

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