zlantanera / prsice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

PRSice

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

NOTE

Please refer to our website for more update instructions

Prerequisite

GCC version 4.8.1 or higher (for c++11) R version 3.2.3 or higher (for plotting)

Installation

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

Rosalind users

You can compile a static version using the following command

git clone https://github.com/choishingwan/PRSice.git
cd PRSice
make

Citation

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