twilight

DOI: 10.18129/B9.bioc.twilight    

Estimation of local false discovery rate

Bioconductor version: Release (3.15)

In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.

Author: Stefanie Scheid <stefanie.scheid at gmx.de>

Maintainer: Stefanie Scheid <stefanie.scheid at gmx.de>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("twilight")

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("twilight")

 

PDF	R Script	Estimation of Local False Discovery Rates
PDF		Reference Manual

Details

biocViews	DifferentialExpression, Microarray, MultipleComparison, Software
Version	1.72.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 17.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0)
Imports	Biobase, graphics, grDevices, stats
LinkingTo
Suggests	golubEsets(>= 1.4.2), vsn(>= 1.7.2)
SystemRequirements
Enhances
URL	http://compdiag.molgen.mpg.de/software/twilight.shtml
Depends On Me	OrderedList
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	twilight_1.72.0.tar.gz
Windows Binary	twilight_1.72.0.zip (64-bit only)
macOS Binary (x86_64)	twilight_1.72.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/twilight
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/twilight
Package Short Url	https://bioconductor.org/packages/twilight/
Package Downloads Report	Download Stats