PRSice-2

PRSice-2

PRSice-2 is a clumping and thresholding-based tool used for calculating Polygenic Risk Scores (PRS) across a range of p-value thresholds.

In this project, PRSice-2 was applied to the UK Biobank dataset to:

• Benchmark PRS results alongside pgsc_calc and PRScs
• Generate scores across multiple p-value thresholds

Installation

• Requirements: R and PLINK 2.0

Download the executable:

wget https://github.com/choishingwan/PRSice/releases/download/2.3.5/PRSice_linux.zip
unzip PRSice_linux.zip
chmod +x PRSice_linux

The following packages are needed in R:

install.packages("data.table")
install.packages("ggplot2")
install.packages("pROC")
install.packages("optparse")
install.packages("broom")

Input files

1. Base (GWAS) data: Summary statistics file with SNPs and their effect sizes
2. Target data: Genotype data in PLINK Binary or BGEN format
3. Phenotype : Individual IDs with their case/control information

Output files

1. Bar Plot for various p-value thresholds
2. High Resolution Plot for various p-value thresholds
3. Quantile Plot with increasing PRS
4. .prsice file with the PRS Model fit
5. .summary file
6. .log file for each run
7. .best file with final PRS for each individual

Sample Command

Rscript PRSice.R \
--base <gwas> \
--target <genotypes> \
--pheno <phenotype file> \
--binary-target <T/F> \
--prsice PRSice_linux \
--out <output_dir>

Additional flags can be included depending on the phenotype, datasets and analysis goals.