create_select_snps_args: Create the command-line arguments to select SNPs

In richelbilderbeek/plinkr: Interface to PLINK

Create the command-line arguments to select SNPs

Description

Create the command-line arguments to select SNPs.

Usage

create_select_snps_args(
  plink_bin_filenames,
  snp_selector,
  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.
snp_selector	a SNP selector, a way to select one or more SNPs. See create_snps_selector for all SNP selectors.
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_snps_args(
  plink_bin_filenames = create_test_plink_bin_filenames(),
  snp_selector = create_test_single_snp_selector()
)
create_select_snps_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")
  ),
  snp_selector = create_test_random_snps_selector()
)
create_select_snps_args(
  plink_bin_filenames = create_test_plink_bin_filenames(),
  snp_selector = create_test_snp_range_selector()
)
create_select_snps_args(
  plink_bin_filenames = create_test_plink_bin_filenames(),
  snp_selector = create_test_snp_window_selector()
)

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