EmpiricalBrownsMethod

This package is for version 3.12 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: 3.12

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>

Citation (from within R, enter citation("EmpiricalBrownsMethod")):

Installation

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


if (!require("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")
Empirical Browns Method HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Pathways, Software, StatisticalMethod
Version 1.18.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License MIT + file LICENSE
Depends R (>= 3.2.0)
Imports
System Requirements
URL https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM.git
See More
Suggests BiocStyle, testthat, knitr, rmarkdown
Linking To
Enhances
Depends On Me poolVIM
Imports Me EBSEA, NADfinder
Suggests Me ActivePathways
Links To Me
Build Report Build Report

Package Archives

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

Source Package EmpiricalBrownsMethod_1.18.0.tar.gz
Windows Binary EmpiricalBrownsMethod_1.18.0.zip
macOS 10.13 (High Sierra) EmpiricalBrownsMethod_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EmpiricalBrownsMethod
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EmpiricalBrownsMethod
Bioc Package Browser https://code.bioconductor.org/browse/EmpiricalBrownsMethod/
Package Short Url https://bioconductor.org/packages/EmpiricalBrownsMethod/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive