globaltest

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

Bioconductor version: 2.7

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 <j.j.goeman at lumc.nl> and Jan Oosting <j.oosting at lumc.nl>

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
System Requirements
License GPL (>= 2)
URL http://www.msbi.nl/goeman
Depends On Me GlobalAncova
Imports Me SIM
Suggests Me topGO
Version 5.4.0
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source globaltest_5.4.0.tar.gz
Windows Binary globaltest_5.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary globaltest_5.4.0.tgz
Package Downloads Report Download Stats

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