| Function | Description |
| exfdr | Example of twilight result |
| expval | Example of twilight.pval result |
| plot.twilight | A plot function for twilight objects |
| print.twilight | A print function for twilight objects |
| twilight | Estimation of local false discovery rate |
| twilight.combi | All permutations of a binary vector |
| twilight.filtering | A function for permutation filtering |
| twilight.permute.pair | A permutation matrix of paired class labels |
| twilight.permute.unpair | A permutation matrix of unpaired class labels |
| twilight.pval | A function to compute p-values from expression sets |