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We have now got a new document page here and we will slowly phase out our wiki page once we have iron out the new document's language and content
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 unimputed 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 | v2.1.0.beta |
| OS X 64-bit | v2.1.0.beta |
| Windows 64-bit | v2.1.0.beta |
Note: PRSice-2 is currently under open beta
To plot graphs, PRSice requires R (version 3.2.3+) installed.
Additional steps might be required for MAC and Window users.
NOTE: All required packages can be automatically downloaded by PRSice using the --dir option.
For Quick start use, please refer to this page
You can also simply call the PRSice executable without any parameter to or with --h to view all available parameters
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. You can help us to speed up the debug process by including the log file generated by PRSice.
For more details on the authors, see:
PRSet is developed and test run by Yunfeng Ruan
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 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 Eigen C++ library.