# 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:

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)
9. PRSet: function for calculating PRS across user-defined pathways / gene sets

Linux 64-bit v2.3.1.e
OS X 64-bit v2.3.1.e
Windows 32-bit Not available
Windows 64-bit Not available

Latest Update

# 2020-05-30 (v2.3.1.e)¶

• Fix bug where SNPs without missingness will be wrongly considered as having 100% missingness
• Fix error log where PRSice should now correct stat if a parameter is missing the required arguments

# 2020-05-29 (v2.3.1.d)¶

• Fix segmentation fault when --ld is used

# 2020-05-28 (v2.3.1.c)¶

• Fix problem with missing covariate
• Fix Rscript such that it properly read in phenotype file when --pheno-col is specified

# 2020-05-26 (v2.3.1.b)¶

• Fix best score output when --ignore-fid is used
• Also fix Rscript covariate and phenotype file read when handling IDs start with 00 and when --ignore-fid is used

# 2020-05-26 (v2.3.1a)¶

• Fix bar plot with covariate. Was plotting the full R2 instead of the PRS.R2

# 2020-05-23 (v2.3.1)¶

• Update Rscript such that it match features in executable (thus avoid problem in plotting)
• Fix a bug where PRSice will crash when there are missing covariates

# 2020-05-18 (v2.3.0)¶

• 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"
• Introduced --chr-id which generate rs id based on user provided formula (see detail for more info)
• Format of --base-maf and --base-info are now changed to <name>:<value> from <name>,<value>
• If user provided the --stat information, 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

Caution

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.

Caution

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.

# 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

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.

## 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:

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 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.