EmpiricalBrownsMethod

This package is for version 3.7 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: 3.7

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 "3.5") 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 1.8.0
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
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Suggests BiocStyle, testthat, knitr, rmarkdown
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Package Archives

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

Source Package EmpiricalBrownsMethod_1.8.0.tar.gz
Windows Binary EmpiricalBrownsMethod_1.8.0.zip
Mac OS X 10.11 (El Capitan) EmpiricalBrownsMethod_1.8.0.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/
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Old Source Packages for BioC 3.7 Source Archive