PRSice-2: Polygenic Risk Score software

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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:

  1. High-resolution scoring (PRS calculated across a large number of P-value thresholds)
  2. Identify Most predictive PRS
  3. Empirical P-values output (not subject to over-fitting)
  4. Genotyped (PLINK binary) and imputed (Oxford bgen v1.2) data input
  5. Biobank-scale genotyped data can be analysed within hours
  6. Incorporation of covariates
  7. Application across multiple target traits simultaneously
  8. Results plotted in several formats (bar plots, high-res plots, quantile plots)

Executable downloads

Operating System Link
Linux 64-bit v2.1.2.beta
OS X 64-bit v2.1.2.beta
Windows 64-bit v2.1.2.beta

Caution

PRSice-2 is currently under open beta - results output are reliable but please report any specific problems to our google group (see Support below)

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.

Quick Start

For Quick start use, please refer to Quick Start

List user options

You can also type

./PRSice

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

Detailed Guide

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

Citation

If you use PRSice, then please cite:

Citation

PRSice: Polygenic Risk Score software, Euesden, Lewis, O'Reilly, Bioinformatics (2015) 31 (9):1466-1468

Support

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.

Authors

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:

Acknowledgement

PRSice is a software package written in C++ (main) and R (plotting). The code relies partially on those 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, the gzstream library and mingw-std-threads.