twilight: Estimation of local false discovery rate

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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@gmx.de>
Date of publication
None
Maintainer
Stefanie Scheid <stefanie.scheid@gmx.de>
License
GPL (>= 2)
Version
1.50.0
URLs

View on Bioconductor

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'

Files in this package

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