PRSice (pronounced 'precise') is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to linkage disequilibrium and P-value ("clumping"), and can be applied across multiple traits in a single run.
Based on a permutation study we estimate a significance threshold of P = 0.001 for high-resolution PRS analyses - the work on this is included in our Bioinformatics paper on PRSice.
PRSice is a software package written in R and C++. PRSice runs as a command-line program with a variety of user-options and is freely available for download below, compatible for Unix/Linux/Mac OS
Please refer to our website for more update instructions
GCC version 4.8.1 or higher (for c++11) R version 3.2.3 or higher (for plotting)
You can directly download the binary files here. If you want to install PRSice, all you have to do is (The binary file will located in PRSice)
git clone https://github.com/choishingwan/PRSice.git cd PRSice g++ --std=c++11 -I inc/ -isystem lib/ -DNDEBUG -O3 -march=native src/*.cpp -lz -lpthread -o PRSice
Or if you have CMake version 3.1 or higher, you can do (The binary file will located in PRSice/bin)
git clone https://github.com/choishingwan/PRSice.git cd PRSice mkdir build cd build cmake ../ make
You can compile a static version using the following command
git clone https://github.com/choishingwan/PRSice.git cd PRSice make
If you PRSice in any published work, please cite the following manuscript:
Choi SW, and O’Reilly PF. "PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data." GigaScience 8, no. 7 (July 1, 2019). https://doi.org/10.1093/gigascience/giz082.
Note to Self
PLINK PRS range is inclusive. e.g. 0 - 0.5 includes also SNPs with p-value of 0 and 0.5