compbio/prsice

•Updated almost 11 years ago

PRSice: calculating polygenic risk scores

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compbio/prsice repository overview

⁠PRSice: Polygenic Risk Score software

PRSice (pronounced 'precise') a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

Publised:Bioinformatics⁠
Software: PRSice
Version: 1.2
Authors:
- Jack Euesden [email protected]⁠
- Cathryn M. Lewis [email protected]⁠
- Paul F. O'Reilly [email protected]⁠
Website: http://PRSice.info⁠

Summary: A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study (GWAS). The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice (‘precise’), for calculating, applying, evaluating and plotting the results of polygenic risk scores. PRSice can calculate PRS at a large number of thresholds (“high resolution”) to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin SNPs according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on Schizophrenia, Major Depressive Disorder and Smoking, illustrate the importance of identifying the best-fit PRS, and estimate a P-value significance threshold for high-resolution PRS studies.

Availability: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimise computational time. PRSice runs as a command-line program with a variety of user-options

⁠PRSice: Dockerised⁠ for your polygenic pleasure!

Here we provide a Docker image of PRSice v1.1 for you to run on your Windows or Mac or Linux box.

⁠Dockered by:

Read the Docs!
The Vignette: PRSice_VIGNETTE_v1.2.pdf⁠

⁠Get me the Docker Version

Intsall docker

Windows: https://docs.docker.com/installation/windows/⁠
Mac: https://docs.docker.com/installation/mac/⁠

Build from scratch

If on Windows or Mac then start boot2docker

## eg on Mac
boot2docker start

docker pull compbio/prsice:1.2

⁠Runnig PRSice

Plink Versions The following PLINK executables are provided and installed in the docker images at :-

/usr/local/bin/plink1.9_i686
/usr/local/bin/plink1.9_x86_64

Make sure you use the right binary for your system eg 64bit vx 32bit!

Running PRSice on a 64bit machine (x86_64)

See user docs or details on running PRSice:
The Vignette: PRSice_VIGNETTE_v1.2.pdf⁠

## make dir for your data
#
mkdir ${HOME}/pgrs
cd ${HOME}/pgrs

## run compbio/prsice:1.2
#
docker \
        run \
        --rm=true \
        -v ${HOME}/pgrs:/home/pipeman \
        --name prsice \
        -i \
        -t compbio/prsice:1.2 \
        R \
        -q \
        --file=/usr/local/bin/PRSice_v1.2.R \
        --args \
        plink /usr/local/bin/plink1.9_x86_64 \
        base /usr/local/bin/TOY_BASE_GWAS.assoc \
        target /usr/local/bin/TOY_TARGET_DATA \
        slower 0 \
        supper 0.5 \
        sinc 0.01 \
        covary F \
        figname /home/pipeman/EXAMPLE_1

⁠Example Output

The first two figures are based on a PRSice run over PGC Schizophrenia and RADIANT-UK Major Depressive Disorder data, as shown in our paper, while the quantile plot is produced from simulated data.

fig1