Package: twilight
Version: 1.89.0
Title: Estimation of local false discovery rate
Authors@R: person(given="Stefanie",family="Senger",
  email="stefanie.scheid@gmx.de",role=c("cre","aut"),
  comment=c(ORCID="0000-0003-4144-1040"))
Description: 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.
Depends: R (>= 2.10)
Imports: Biobase, graphics, grDevices, splines, stats
Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2)
License: GPL (>= 2)
URL: http://compdiag.molgen.mpg.de/software/twilight.shtml
biocViews: Microarray, DifferentialExpression, MultipleComparison
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:30:47 UTC
RemoteUrl: https://github.com/bioc/twilight
RemoteRef: HEAD
RemoteSha: 4e7790e2647544a79f3b6507d2ceb433d4a6a3c0
NeedsCompilation: yes
Packaged: 2026-07-19 05:15:20 UTC; root
Author: Stefanie Senger [cre, aut] (ORCID:
    <https://orcid.org/0000-0003-4144-1040>)
Maintainer: Stefanie Senger <stefanie.scheid@gmx.de>