cfdr.pleio

The cfdr.pleio package implements conditional and conjunctional false discovery rates to leverage and study pleiotropic gene variants between pairs of phenotypic traits, as originally described by Andreassen et al. (2013).

Installation

You can install the development version of cfdr.pleio like so:

if ( !require("remotes", quietly = TRUE) ) install.packages("remotes")
remotes::install_github("alexploner/cfdr.pleio", build_vignettes = TRUE)

cfdr.pleio also needs a set of genetic reference data in a local directory; you can download a local copy like so:

download.file("https://zenodo.org/record/5750318/files/genref.zip",
               destfile = "/path/to/dir/genref.zip")
unzip("/path/to/dir/genref.zip", exdir = "/path/to/dir")               

You can delete the zip file after successful unpacking.

Example

For a basic example, install the package and read the introductory vignette:

vignette("Introduction", package = "cfdr.pleio")

Credit

cfdr.pleio is a based on a fork (in February 2021) of the MATLAB package pleiofdr available from https://github.com/precimed/pleiofdr