This repository contains the code to reproduce the results in Marginal false discovery rates for penalized regression models, by Patrick Breheny.
The mfdr function, which actually calculates the marginal false discovery rates, is implemented in ncvreg.
If you are familiar with the make utility, using this repository is straightforward:
make Fig4
makes Figure 4, and so on (the file Fig4.pdf will appear in the fig/ directory).
If you are not familiar with make, Karl Broman has a helpful primer here, or you can run the R code manually: Fig2.R has the code for creating Figure 2, and so on. Note that many of the figures are based on simulations, so you'll have to generate the output with the code in Sim2.R before you can plot it.
If you have any questions, please contact me.
Note: Due to restrictions on the sharing of human genetic data, I am unable to provide the data necessary to reproduce the analyses in Section 6.3. All other analyses in the manuscript are covered by this repository.