Our guide paper is now published in Nature Protocols:
Choi, S.W., Mak, T.S. & O’Reilly, P.F. Tutorial: a guide to performing polygenic risk score analyses. Nat Protoc (2020). https://doi.org/10.1038/s41596-020-0353-1
The online tutorial that accompanies the paper is here
PRSice-2: Polygenic Risk Score software
PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. Some of the features include:
- High-resolution scoring (PRS calculated across a large number of P-value thresholds)
- Identify Most predictive PRS
- Empirical P-values output (not subject to over-fitting)
- Genotyped (PLINK binary) and imputed (Oxford bgen v1.2) data input
- Biobank-scale genotyped data can be analysed within hours
- Incorporation of covariates
- Application across multiple target traits simultaneously
- Results plotted in several formats (bar plots, high-res plots, quantile plots)
- PRSet: function for calculating PRS across user-defined pathways / gene sets
|OS X 64-bit||v2.3.3|
|Windows 32-bit||Not available|
|Windows 64-bit||Not available|
- Thanks to report from @charlisech, we were able to pinpoint a bug related to sample selection when using bgen data.
- We now support multi-threaded clumping (separated by chromosome)
- Genotypes will be stored to memory during clumping (increase memory usage, significantly speed up clumping)
- Will only generate one .prsice file for all phenotypes
- .prsice file now has additional column call "Pheno"
--chr-idwhich generate rs id based on user provided formula (see detail for more info)
- Format of
--base-infoare now changed to
- If user provided the
--statinformation, PRSice will now error out instead of trying to look for BETA or OR in the file.
update log for previous release can be found here
We have now fixed window problem. But was unable to access the computer that is used for compilation due to COVID. Will try to compile it when we regain access.
PRSet are currently under open beta - results output are reliable but please report any specific problems to our google group (see Support below)3
R Packages Requirements
To plot graphs, PRSice requires R (version 3.2.3+) installed.
Additional steps might be required for Mac and Windows users.
Installing required R packages
PRSice can automatically download all required packages, even without administrative right.
You can specify the install directory using
--dir. For example
Rscript PRSice.R --dir .
will install all required packages under the local directory.
For Quick start use, please refer to Quick Start
List user options
You can also type
to view all available parameters unrelated to plotting, or
Rscript PRSice.R -h
to view all available parameters, including those used for plotting
Output of Results
You can see the expected output of PRSice here
You can find a more detailed document explaining the input and output of PRSice in this page
Full command line options
You can find all command line options of PRSice under the section Details of PRSice/PRSet
If you use PRSice, then please cite:
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.
This wiki should contain all the basic instruction for the use of PRSice. Shall you have any problems, please feel free to start an issue here or visit our google group. You can help us to speed up the debug process by including the log file generated by PRSice.
In addition, you can use the search bar in this webpage to search for specific functions.
For more details on the authors, see:
PRSice-2 and all new functionalities are coded by:
PRSice is a software package written in C++ (main) and R (plotting). The code relies partially on those written in PLINK by Christopher Chang. Management of BGEN file is based on BGEN lib written by Gavin Band. We also utilize the Eigen C++ library, the gzstream library.