Preparation

Before performing PRSice, quality control should be performed on the target samples. See here for an example.

Input

  • PRSice.R file: A wrapper for the PRSice executable and for plotting
  • PRSice executable 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

Running PRSice

In most case, assuming the PRSice executable is located in ($HOME)/PRSice/ and the working directory is ($HOME)/PRSice, you can run PRSice with the following commands:

Note

For window users, please use Rscript.exe instead of Rscript

Important

Do not copy codes to Microsoft Word. Word has a tendency to change characters from codes into special characters that cannot be recognized by the terminal

Binary Traits

For binary traits, the following command can be used (commands specific to binary traits are highlighted in yellow)

Rscript PRSice.R --dir . \
    --prsice ./PRSice \
    --base TOY_BASE_GWAS.assoc \
    --target TOY_TARGET_DATA \
    --thread 1 \
    --stat OR \
    --binary-target T

Rscript.exe PRSice.R --dir . ^
    --prsice ./PRSice.exe ^
    --base TOY_BASE_GWAS.assoc ^
    --target TOY_TARGET_DATA ^
    --thread 1 ^
    --stat OR ^
    --binary-target T

Quantitative Traits

For quantitative traits, the following can be used instead (commands specific to quantitative traits are highlighted in yellow)

Rscript PRSice.R --dir . \
    --prsice ./PRSice \
    --base TOY_BASE_GWAS.assoc \
    --target TOY_TARGET_DATA \
    --thread 1 \
    --stat BETA \
    --beta \
    --binary-target F

Rscript.exe PRSice.R --dir . ^
    --prsice ./PRSice.exe ^
    --base TOY_BASE_GWAS.assoc ^
    --target TOY_TARGET_DATA ^
    --thread 1 ^
    --stat BETA ^
    --beta ^
    --binary-target F

Note

If the type of Effect (--stat) or data type (--binary-target) were not specified, PRSice will try to determine these information based on the header of the base file:

  1. When BETA (case insensitive) is found in the header and --stat was not provided, --beta will be added to the command, and if --binary-target was not provided, --binary-target F will be added to the command

  2. When OR (case insensitive) is found in the header and --binary-target was not provided, --or will be added to the command, and if --binary-target was not provided, --binary-target T will be added to the command

  3. PRSice cannot determine if the type of effect / data type if the base file contains both OR and BETA

PRSice will detail all effective options in its log file.

Quality Control of Target Samples

Quality controls can be performed on the target samples using PLINK. A good starting point is (assume ($target) is the prefix of the target binary file)

plink --bfile ($target) \
    --maf 0.05 \
    --mind 0.1 \
    --geno 0.1 \
    --hwe 1e-6 \
    --make-just-bim \
    --make-just-fam \
    --out ($target).qc

plink.exe --bfile ($target) ^
    --maf 0.05 ^
    --mind 0.1 ^
    --geno 0.1 ^
    --hwe 1e-6 ^
    --make-just-bim ^
    --make-just-fam ^
    --out ($target).qc

Then, --keep ($target).qc.fam --extract ($target).qc.bim can be added to the PRSice command to filter out the samples and SNPs.

You can refer to Marees et al (2018) for a more detail guide. You can also find our PRS tutorial here.