twilight: Estimation of local false discovery rate
Version 1.52.0

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.

AuthorStefanie Scheid <stefanie.scheid@gmx.de>
Bioconductor views DifferentialExpression Microarray MultipleComparison
Date of publicationNone
MaintainerStefanie Scheid <stefanie.scheid@gmx.de>
LicenseGPL (>= 2)
Version1.52.0
URL http://compdiag.molgen.mpg.de/software/twilight.shtml
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("twilight")

Popular man pages

exfdr: Example of twilight result
plot.twilight: Plot function for twilight objects
print.twilight: Print function for twilight objects
twilight.getlambda: Internal function to compute regularization parameter lambda
twilight.getmatrix: Internal function to extract the gene expression matrix from...
twilight.permute.unpair: Permutation matrix of unpaired class labels
twilight.teststat: Interface to the test statistics provided within 'twilight'
See all...

All man pages Function index File listing

Man pages

exfdr: Example of twilight result
expval: Example of twilight.pval result
plot.twilight: Plot function for twilight objects
print.twilight: Print function for twilight objects
twilight: Estimation of the local false discovery rate
twilight.combi: All permutations of a binary vector
twilight.filtering: Permutation filtering
twilight.getlambda: Internal function to compute regularization parameter lambda
twilight.getmatrix: Internal function to extract the gene expression matrix from...
twilight.permute.pair: Permutation matrix of paired class labels
twilight.permute.unpair: Permutation matrix of unpaired class labels
twilight.pval: Compute p-values from expression sets
twilight.teststat: Interface to the test statistics provided within 'twilight'

Functions

First.lib Source code
exfdr Man page
expval Man page
plot.twilight Man page Source code
print.twilight Man page Source code
twilight Man page Source code
twilight.combi Man page Source code
twilight.filtering Man page Source code
twilight.getlambda Man page Source code
twilight.getmatrix Man page Source code
twilight.permute.pair Man page Source code
twilight.permute.unpair Man page Source code
twilight.pval Man page Source code
twilight.teststat Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/a.R
R/plot.twilight.R
R/print.twilight.R
R/twilight.R
R/twilight.combi.R
R/twilight.filtering.R
R/twilight.getlambda.R
R/twilight.getmatrix.R
R/twilight.permute.pair.R
R/twilight.permute.unpair.R
R/twilight.pval.R
R/twilight.teststat.R
build
build/vignette.rds
data
data/exfdr.rda
data/expval.rda
inst
inst/R-script
inst/R-script/makedata.R
inst/doc
inst/doc/tr_2004_01.R
inst/doc/tr_2004_01.Rnw
inst/doc/tr_2004_01.pdf
man
man/exfdr.Rd
man/expval.Rd
man/plot.twilight.Rd
man/print.twilight.Rd
man/twilight.Rd
man/twilight.combi.Rd
man/twilight.filtering.Rd
man/twilight.getlambda.Rd
man/twilight.getmatrix.Rd
man/twilight.permute.pair.Rd
man/twilight.permute.unpair.Rd
man/twilight.pval.Rd
man/twilight.teststat.Rd
src
src/confidence.line.c
src/correlation.c
src/kstest.c
src/sep.c
src/twosample.perm.c
src/twosample.single.c
vignettes
vignettes/MPIMG_logo.png
vignettes/Makefile
vignettes/Rplots.pdf
vignettes/bcb_logo.pdf
vignettes/compdiag.sty
vignettes/tr_2004_01.Rnw
vignettes/tr_2004_01.tex
vignettes/twilight_slide.ppt
twilight documentation built on May 20, 2017, 10:11 p.m.

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