# twilight v1.42.0

## 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.

## Functions in twilight

 Name Description twilight.combi All permutations of a binary vector print.twilight Print function for twilight objects twilight Estimation of the local false discovery rate twilight.permute.pair Permutation matrix of paired class labels plot.twilight Plot function for twilight objects twilight.filtering Permutation filtering twilight.getlambda Internal function to compute regularization parameter lambda twilight.getmatrix Internal function to extract the gene expression matrix from an expression set exfdr Example of twilight result expval Example of twilight.pval result twilight.teststat Interface to the test statistics provided within 'twilight' twilight.permute.unpair Permutation matrix of unpaired class labels twilight.pval Compute p-values from expression sets No Results!