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
- SNP file: A file containing SNPs constituting the gene set of interest. Can be in MSigDB (gmt) format or a file contain a single column of SNP IDs.
In most case, assuming the PRSice binary is located in
($HOME)/PRSice/bin/ and the working directory is
($HOME)/PRSice, you can run PRSet with the following commands:
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:SetA,B.bed \ --multi-plot 10
Both bed and GTF+MSigDB input can be used together
Name of the set will be the bed file name or can be provided using
With SNP Set
Finally, if you want to construct sets based on a list of SNPs, you can use
Rscript PRSice.R \ --prsice ./bin/PRSice \ --base TOY_BASE_GWAS.assoc \ --target TOY_TARGET_DATA \ --binary-target T \ --thread 1 \ --snp-set A.snp:A,B.snp \ --multi-plot 10
Two different format are allowed:
- SNP Set list format: A file containing a single column of SNP ID. Name of the set will be the file name or can be provided using
- MSigDB format: Each row represent a single SNP set with the first column containing the name of the SNP set.