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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("twilight")
In most cases, you don't need to download the package archive at all.
twilight
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Estimation of local false discovery rate
Bioconductor version: Release (3.5)
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 (from within R,
enter citation("twilight")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("twilight")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("twilight")
| R Script | Estimation of Local False Discovery Rates | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, Microarray, MultipleComparison, Software |
| Version | 1.52.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 12.5 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 | OrderedList |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | twilight_1.52.0.tar.gz |
| Windows Binary | twilight_1.52.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | twilight_1.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/twilight |
| Package Short Url | http://bioconductor.org/packages/twilight/ |
| Package Downloads Report | Download Stats |
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