# Background¶

A new feature of PRSice is the ability to perform set base/pathway based analysis. This new feature is called PRSet.

Paper on PRSet currently under preparation.

Important

PRSet is currently under active development. Notably, the current version of PRSet available here only provides self-contained pathway results, which eg. do not account for pathway size. We are presently testing the power of PRSet Vs alternative pathway methods, so for now recommend assuming that other leading pathway approaches (eg. MAGMA) are most powerful for identification of causal pathways.

# Preparation¶

PRSet is mainly based on PRSice. To perform PRSet, you will need the following inputs

## Input¶

• PRSice.R file: A wrapper for the PRSice binary and for plotting
• PRSice binary file: Perform all analysis except plotting
• Base data set: GWAS summary results, which the PRS is based on
• Target data set: Raw genotype data of "target phenotype". Can be in the form of PLINK binary or BGEN

## PRSet Specific Input¶

• Bed file(s): Bed file(s) containing region of genes within a gene set; or
• MSigDB file: File containing name of each gene sets and the ID of genes within the gene set on each individual line. If MSigDB is provided, GTF file is required.
• GTF file: A file contain the genome boundary of each individual gene

Note

Currently, it is recommended to perform MAGMA to identify significant gene sets and use those as an input of PRSet

# Running PRSet¶

In most case, you can simply run PRSice using the following command, assuming your PRSice binary is located in ($HOME)/PRSice/bin/ and you are working in ($HOME)/PRSice

## With MSigDB data¶

Assuming you have downloaded a MSigDB file (set.txt) and a gene gtf file (gene.gtf) from Ensemble, then you can run PRSet with the following command

Rscript PRSice.R \
--prsice ./bin/PRSice \
--base TOY_BASE_GWAS.assoc \
--target TOY_TARGET_DATA \
--binary-target T \
--gtf gene.gtf \
--msigdb set.txt \
--multi-plot 10


This will perform PRSet analysis and generate the multi-set plot with the top 10 gene sets

## With Bed Files¶

Alternatively, if you have a list of bed files e.g. A.bed,B.bed as an input, you can run PRSet as

Rscript PRSice.R \
--prsice ./bin/PRSice \
--base TOY_BASE_GWAS.assoc \
--target TOY_TARGET_DATA \
--binary-target T \