EmpiricalBrownsMethod
This is the development version of EmpiricalBrownsMethod; for the stable release version, see EmpiricalBrownsMethod.
Uses Brown's method to combine p-values from dependent tests
Bioconductor version: Development (3.24)
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("EmpiricalBrownsMethod")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Pathways, Software, StatisticalMethod |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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 |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EmpiricalBrownsMethod_1.41.0.tar.gz |
| Windows Binary (x86_64) | EmpiricalBrownsMethod_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | EmpiricalBrownsMethod_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | EmpiricalBrownsMethod_1.41.0.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 |