create_select_samples_args: Create the command-line arguments to select samples

In richelbilderbeek/plinkr: Interface to PLINK

Create the command-line arguments to select samples

Description

Create the command-line arguments to select samples.

Usage

create_select_samples_args(
  plink_bin_filenames,
  sample_selector,
  sample_ids_filename = plinkr::get_plinkr_tempfilename(pattern = "sample_ids_",
    fileext = ".txt"),
  base_output_filename = plinkr::get_plinkr_tempfilename(),
  plink_options = create_plink_options()
)

Arguments

plink_bin_filenames	the binary data files' names for PLINK to work on, as created by create_plink_bin_filenames.
sample_selector	a sample/individual selector, a way to select one or more samples/individuals. See create_samples_selector for all sample selectors.
sample_ids_filename	name of a file to store sample_ids (see check_sample_ids) to
base_output_filename	the base of the filenames that are used as output for PLINK/PLINK2
plink_options	options to run PLINK, as created by create_plink_options

Value

the command-line arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

create_select_samples_args(
  plink_bin_filenames = create_test_plink_bin_filenames(),
  sample_selector = create_test_single_sample_selector()
)
create_select_samples_args(
  plink_bin_filenames = create_plink_bin_filenames(
    bed_filename = get_plinkr_filename("select_snps.bed"),
    bim_filename = get_plinkr_filename("select_snps.bim"),
    fam_filename = get_plinkr_filename("select_snps.fam")
  ),
  sample_selector = create_test_random_samples_selector()
)

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