twilight
This is the development version of twilight; for the stable release version, see twilight.
Estimation of local false discovery rate
Bioconductor version: Development (3.21)
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>
citation("twilight")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| Estimation of Local False Discovery Rates | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, Microarray, MultipleComparison, Software |
| Version | 1.83.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 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 |
| System Requirements | |
| URL | http://compdiag.molgen.mpg.de/software/twilight.shtml |
See More
| Suggests | golubEsets(>= 1.4.2), vsn(>= 1.7.2) |
| Linking To | |
| Enhances | |
| Depends On Me | OrderedList |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | twilight_1.83.0.tar.gz |
| Windows Binary (x86_64) | twilight_1.83.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/twilight |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/twilight |
| Bioc Package Browser | https://code.bioconductor.org/browse/twilight/ |
| Package Short Url | https://bioconductor.org/packages/twilight/ |
| Package Downloads Report | Download Stats |