run_plink: Run PLINK from arguments

In richelbilderbeek/plinkr: Interface to PLINK

Run PLINK from arguments

Description

Run PLINK from arguments

Usage

run_plink(args, plink_options = create_plink_options(), verbose = FALSE)

Arguments

args	arguments for the PLINK or PLINK2 executable. Use check_plink_args to check if these are valid
plink_options	options to run PLINK, as created by create_plink_options
verbose	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Value

the text that PLINK returns

Author(s)

Richèl J.C. Bilderbeek

Examples

# Minimal example: show the PLINK help
if (is_plink_installed(create_plink_v1_7_options())) {
  # Without '--noweb', plinkr freezes with PLINK v1.7
  run_plink(
    args = c("--help", "--noweb"),
    create_plink_v1_7_options()
  )
}

if (is_plink_installed(create_plink_v1_9_options())) {
  run_plink("--help", create_plink_v1_9_options())
}

if (is_plink_installed(create_plink_v2_0_options())) {
  run_plink("--help", create_plink_v2_0_options())
}

# Do a case-control association
# Note: using 'plinkr::assoc' is safer, easier and has a uniform
# interface accross PLINK versions
plink_options <- create_plink_v1_9_options()
if (is_plink_installed(plink_options)) {

  # Use the PLINK v1.9 example files
  ped_filename <- get_plink_example_filename(
    "toy.ped", plink_options
 )
  map_filename <- get_plink_example_filename(
    "toy.map", plink_options
  )

  run_plink(
    args = c(
     "--ped", ped_filename,
     "--map", map_filename
    ),
    plink_options
  )

  # Delete the created files
  file.remove("plink.bed")
  file.remove("plink.fam")
  file.remove("plink.log")
}

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.