Screenshot

Requirements

BridgePRS uses R (\(\geq\) 3.6.3), plink, and runs using a python3 wrapper.

R packages

BridgePRS requires the following R packages:
BEDMatrix, boot, data.table, doMC, glmnet, MASS, optparse, parallel, and R.utils

R Packages

These packages can be installed from inside an R terminal using the command: 

$ R 
install.packages(c("BEDMatrix","boot","data.table","doMC","glmnet","MASS","optparse","parallel","R.utils"))

Plink documentation and downlaod can be found here.

The BridgePRS downlaod includes plink for Linux and MacOs and the software will attempt to locate the correct version. To override this behaviour and use a specific version please use the flag --plinkPath $PLINKPATH to direct BridgePRS to the file location.

Extra MacOs Security:

MacOs often block executables if they are not approved from the app store. You may have to change your settings to allow Plink to be called
For instructions on how to do so, please click here.

Python

Python3+ can be downloaded here. Optional plots are created using the python library [matplotlib] (https://matplotlib.org/stable/users/installing/index.html)).

Bash

BridgePRS can also be run using a shell script as described here. Shell scripts that run the example data are provided with the download.

BridgePRS check

Once BridgePRS has been downloaded and made executable the following command will check system compatibility and prompt you to install missing software:

./bridgePRS check requirements
Checking Requirements:
System:  platform=linux,  cores(available)=8,          cores(used)=1       (TIP: Using More Than One Core Will Improve Performace (e.g. ---cores 7))
Plink:  found=true,      path=/home/tade/Bin/plink
R:  found=true,      path=/usr/bin/R,             version=3.6.3       (packages=up to date)                                            
Python3:  found=true,      path=/usr/bin/python3,     matplotlib=true
    Complete