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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)
- Most predictive PRS identified
- Genotyped (PLINK binary) and imputed (Oxford bgen v1.2) data input
- Biobank-scale 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)
- Empirical P-values output (not subject to over-fitting)
- PRSet: function for calculating PRS across pathways / gene sets (user list option)
| Operating System | Link |
|---|---|
| Linux 64-bit | v2.0.13.beta |
| Linux 32-bit | download |
| OS X 64-bit | download |
Note: PRSice-2 does not currently support Windows (to appear soon). Note: PRSice-2 is currently under open beta
You will need R for plotting the graphs (compatible with R 3.2.3+).
NOTE: All required packages can be automatically downloaded by PRSice using the --dir option.
For example
Rscript PRSice.R --dir <directory>
will install all required packages in <directory>. To install the packages in the current directory, use . in place of <directory>
For Quick start use, please refer to this page
You can find a more detailed document explaining the input and output of PRSice in this page
You can find all command line options of PRSice in this page
If you use PRSice, then please cite:
PRSice: Polygenic Risk Score software, Euesden, Lewis, O'Reilly, Bioinformatics (2015) 31 (9):1466-1468
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
For more details on the authors, see:
PRSet is developed and test run by Yunfeng Ruan
PRSice-2 and the new functionality coded by:
PRSice is a software package written in C++ (main) and R (plotting). The code relies partially on that written in PLINK by Shaun Purcell and Christopher Chang. Management of BGEN file is based on BGEN lib written by Gavin Band. We also utilize the Boost library and Eigen C++.