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The goal of bayefdr is to provide tools for the estimation andoptimisation of Bayesian expected false discovery and expected falsenegative rates.

You can install the released version of bayefdr fromCRAN with:

install.packages("bayefdr")# development version:## devtools::install_github("VallejosGroup/bayefdr")

The main functions in this package areefdr,efnr andefdr_search.efdr andefnr calculate the EFDR or EFNR for a vector ofprobabilities given a specified probability threshold.efdr_searchfinds the probability threshold that matches a target EFDR as closely aspossible. The basic input to this function is a vector of probabilitiesand a target EFDR.

library("bayefdr")set.seed(42)probs <- runif(100)efdr(0.7, probs)#> [1] 0.1429126efnr(0.7, probs)#> [1] 0.3531349efdr <- efdr_search(probs, target_efdr = 0.1)efdr#> An object of class 'bayefdr'.#>  Optimal threshold: 0.768 EFDR: 0.0985 EFNR: 0.399

The output of this function is adata.frame with some extraattributes. There is a plot method too.

head(efdr)#>   threshold     EFDR      EFNR#> 1   0.50000 0.239581 0.2361073#> 2   0.50025 0.239581 0.2361073#> 3   0.50050 0.239581 0.2361073#> 4   0.50075 0.239581 0.2361073#> 5   0.50100 0.239581 0.2361073#> 6   0.50125 0.239581 0.2361073plot(efdr)