In richelbilderbeek/plinkr: Interface to PLINK

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(plinkr)

In this vignette, I run the PLINK2 commands at https://www.cog-genomics.org/plink/2.0/general_usage using plinkr.

This vignette will give output only if PLINK v1.9 and PLINK2 are installed:

if (!is_plink_installed(create_plink_v1_9_options())) {
  message("PLINK v1.9 is not installed")
  message("Tip: use 'plinkr::install_plinks()'")
}

if (!is_plink_installed(create_plink_v2_0_options())) {
  message("PLINK v2.0 is not installed")
  message("Tip: use 'plinkr::install_plinks()'")
}

The PLINK2 website verifies both PLINK and PLINK2:

./plink --dummy 2 2 --freq --make-bed --out toy_data
./plink2 --bfile toy_data --freq --out test2

The first line creates a dummy .bed file using PLINK, the second line reads that .bed file using PLINK2.

In plinkr:

if (is_plink_installed(create_plink_v1_9_options())) {
  run_plink(
    args = c("--dummy", "2", "2", "--freq", "--make-bed", "--out", "toy_data"),
    plink_options = create_plink_v1_9_options()
  )
  plink_toy_data_files <- list.files(pattern = "toy_data", full.names = TRUE)
  plink_toy_data_files
}

if (is_plink_installed(create_plink_v2_0_options())) {
  run_plink(
    args = c("--bfile", "toy_data", "--freq", "--out", "test2"),
    plink_options = create_plink_v2_0_options()
  )
  plink2_toy_data_files <- list.files(pattern = "test2", full.names = TRUE)
  plink2_toy_data_files
}

Cleaning up:

if (is_plink_installed(create_plink_v1_9_options())) {
  file.remove(plink_toy_data_files)
}
if (is_plink_installed(create_plink_v2_0_options())) {
  file.remove(plink2_toy_data_files)
}