create_snp_window_selector: Create a SNP window selector

In richelbilderbeek/plinkr: Interface to PLINK

Create a SNP window selector

Description

Create a SNP window selector, to be used in, for example, select_snps

Usage

create_snp_window_selector(snp, window_kb)

Arguments

snp	a SNP, e.g. rs12345678, as can be checked by check_snp
window_kb	the window (i.e. the amount of base pairs around a focal SNP) in kilobases, as checked by check_window_kb

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_test_snp_window_selector to create a SNP window selector to be used in testing.

There are multiple SNP selectors, see create_snps_selector for an overview

Examples

create_snp_window_selector(
  snp = "my_snp",
  window_kb = 12.34
)

if (is_plink_installed()) {

  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")
  )

  # Selects a window of 3, i.e. the variant before,
  # and after the focal SNP
  snp_window_selector <- create_snp_window_selector(
    snp = "snp_5",
    window_kb = 0.003
  )
  new_plink_bin_data <- select_snps(
    data = plink_bin_filenames,
    snp_selector = snp_window_selector
  )
}

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