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.
PRSet is currently under active development.
PRSet is based on PRSice, with additional input requirements
- 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
In most case, PRSet can simply be run using the following command, assuming the
PRSice binary is located in
($HOME)/PRSice/bin/ and the working directory is
With MSigDB data¶
Rscript PRSice.R \ --prsice ./bin/PRSice \ --base TOY_BASE_GWAS.assoc \ --target TOY_TARGET_DATA \ --binary-target T \ --thread 1 \ --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 a list of bed files are available, e.g. A.bed,B.bed, PRSet can be performed by running
Rscript PRSice.R \ --prsice ./bin/PRSice \ --base TOY_BASE_GWAS.assoc \ --target TOY_TARGET_DATA \ --binary-target T \ --thread 1 \ --bed A.bed,B.bed \ --multi-plot 10
Both bed and GTF+MSigDB input can be used together