EmpiricalBrownsMethod

DOI: 10.18129/B9.bioc.EmpiricalBrownsMethod    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EmpiricalBrownsMethod.

Uses Brown's method to combine p-values from dependent tests

Bioconductor version: 3.9

Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.

Author: William Poole

Maintainer: David Gibbs <dgibbs at systemsbiology.org>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("EmpiricalBrownsMethod")

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("EmpiricalBrownsMethod")

 

HTML	R Script	Empirical Browns Method
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, Pathways, Software, StatisticalMethod
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.2.0)
Imports
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM.git
Depends On Me
Imports Me	NADfinder
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	EmpiricalBrownsMethod_1.12.0.tar.gz
Windows Binary	EmpiricalBrownsMethod_1.12.0.zip
Mac OS X 10.11 (El Capitan)	EmpiricalBrownsMethod_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EmpiricalBrownsMethod
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EmpiricalBrownsMethod
Package Short Url	https://bioconductor.org/packages/EmpiricalBrownsMethod/
Package Downloads Report	Download Stats