Calculate PRS
The plink_prs() function can be used to calculate a PRS
using plink2, given a dataframe containing variant ids, effect alleles,
corresponding weights, and a directory containing individual-level
genotypes for the target population.
Here is an example of using the plink_prs() function to
calculate a prs, given weights from weights_df and genotype
information contained in the
/project/PMBB/PMBB-Release-2020-2.0/Imputed/pgen/
directory. The variant ids in the weights_df file should
correspond to the variant ids in the plink files specified by
pfile_dir. This may require the use of a crosswalk between
rsids and chrom:pos:ref:alt, depending on the variant naming conventions
of the base/target datasets.
#' \dontrun{
# load weights file into dataframe
weights_df <- fs::path_package("extdata", "PGS000667-PMBB.txt", package = "prsr") %>%
vroom::vroom()
# calculate prs
prs_res <- plink_prs(
base_df = weights_df,
id_col = variant,
effect_allele_col = effect_allele,
effect_size_col = effect_weight_mg_dl,
pfile_dir = "/project/PMBB/PMBB-Release-2020-2.0/Imputed/pgen/",
plink_bin = "/scratch/Applications/PLINK/plink2_linux_x86_64_20211125/plink2a"
)
#' }