plink2_assoc_on_plink2_bin_files: Let 'PLINK2' detect an association with one binary trait on...

In richelbilderbeek/plinkr: Interface to PLINK

Let PLINK2 detect an association with one binary trait on PLINK2 binary files

Description

Let PLINK2 detect an association with one binary trait on PLINK2 binary files

Usage

plink2_assoc_on_plink2_bin_files(
  assoc_data,
  assoc_params,
  plink_options = create_plink_v2_0_options(),
  verbose = FALSE
)

Arguments

assoc_data	data to use for an association analysis for a quantitative trait (i.e. using assoc), as can be created by create_assoc_data
assoc_params	parameters to do an association analysis for a quantitative trait (i.e. using assoc), as can be created by create_assoc_params
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

a list with the following columns:

• assoc_table: a tibble with associations found by PLINK2. See read_plink_assoc_file for an explanation of the column names.

• log: the log file as text as created by PLINK2

Note

This function is named after the --assoc flag used by PLINK

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_plink_installed()) {

  if (1 == 2) {
    # Need help of 'pgenlibr' to save a .pgen file
    plink2_assoc_on_plink2_bin_files(
      assoc_data = create_assoc_data(create_test_plink2_bin_filenames()),
      assoc_params = create_test_assoc_params()
    )
  }
}

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