get_minor_alelle_frequencies: Get the minor allele frequencies from genetic data

In richelbilderbeek/plinkr: Interface to PLINK

Get the minor allele frequencies from genetic data

Description

Get the minor allele frequencies from genetic data

Usage

get_minor_alelle_frequencies(
  data,
  plink_options = create_plink_options(),
  temp_folder = plinkr::get_plinkr_tempfilename(),
  verbose = FALSE
)

Arguments

data	the data source, which can be: PLINK text data, as created by create_plink_text_data. PLINK binary data, as created by create_plink_bin_data. PLINK2 binary data, as created by create_plink2_bin_data. PLINK text filenames, as created by create_plink_text_filenames. PLINK binary filenames, as created by create_plink_bin_filenames. PLINK2 binary filenames, as created by create_plink2_bin_filenames. data to be used by assoc, as created by create_assoc_data data to be used by assoc_qt, as created by create_assoc_qt_data
plink_options	options to run PLINK, as created by create_plink_options
temp_folder	temporary folder to store results in
verbose	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Value

the minor allele frequecies

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_plink_installed()) {
  assoc_qt_data <- create_demo_assoc_qt_data()

  # PLINK text data
  get_minor_alelle_frequencies(assoc_qt_data$data)

  # PLINK binary data
  assoc_qt_data$data <- convert_plink_text_data_to_plink_bin_data(
    assoc_qt_data$data
  )
  get_minor_alelle_frequencies(assoc_qt_data$data)
}

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