There are a few required and quality of life steps to run before starting to use the simulated data.

First open a BASH command line window and load the latest version of R available on your system: module load R/4.2.1

Next locate your installation of DeepPheWAS or install DeepPheWAS in R now. Packages are by default installed in the home directory in a folder called R and sub folder that represents the R version being used, for our above R installation this would be.

~/R/4.2/DeepPheWAS/

As you can run all of the simulated data in a single interactive window we can define a variable $package and that can be used throughout, use the code below replacing ~/R/4.2/DeepPheWAS with the location of the R package on your system.

package=~/R/4.2/DeepPheWAS

Now locate a directory on your system to save all of the outputs of the PheWAS, we will define this root folder as $phewas_folder, replace /path/to/folder/ with the full path to folder.

phewas_folder=/path/to/folder/

We can now use $package and $phewas_folder throughout the remaining scripts using the simulated data.

Note about --PheWAS_manifest_overide

Throughout many of the example scripts the --PheWAS_manifest_overide argument is used. In normal running of DeepPheWAS this is not required and would not be included in most analyses. It is used as simulated data was only created for 25 phenotypes and so a smaller version of the PheWAS manifest file was created for use in the examples, the default PheWAS manifest file will be appropriate for almost all analyses unless new phenotypes have been coded.