Package: twilight 1.81.0
Stefanie Scheid
twilight: Estimation of local false discovery rate
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.
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twilight.pdf |twilight.html✨
twilight/json (API)
| # Install 'twilight' in R: |
| install.packages('twilight', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:twilight-1.81.0(bioc 3.20)twilight-1.80.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:463ab0352e
Exports:plot.twilightprint.twilighttwilighttwilight.combitwilight.filteringtwilight.getlambdatwilight.getmatrixtwilight.permute.pairtwilight.permute.unpairtwilight.pvaltwilight.teststat
Dependencies:BiobaseBiocGenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Example of twilight result | exfdr |
| Example of twilight.pval result | expval |
| Plot function for twilight objects | plot.twilight |
| Print function for twilight objects | print.twilight |
| Estimation of the local false discovery rate | twilight |
| All permutations of a binary vector | twilight.combi |
| Permutation filtering | twilight.filtering |
| Permutation matrix of paired class labels | twilight.permute.pair |
| Permutation matrix of unpaired class labels | twilight.permute.unpair |
| Compute p-values from expression sets | twilight.pval |
| Interface to the test statistics provided within 'twilight' | twilight.teststat |
