get_marker_correlation_coefficients: Get the marker correlation coefficients (also known as 'r')...

In richelbilderbeek/plinkr: Interface to PLINK

Get the marker correlation coefficients (also known as r) from genetic data.

Description

Similar to PLINK, the correlation coefficients are measured for markers on the same chromosome

Usage

get_marker_correlation_coefficients(
  data,
  ld_window_r2 = 0.2,
  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
ld_window_r2	the minimal squared correlation coefficient (also known as r^2) between markers. This parameter is named after the --ld_window_r2 flag, as documented at https://www.cog-genomics.org/plink/1.9/ld.
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 marker correlation coefficients, which will be in range ⁠[ld_window_r2, 1.0]⁠ and ⁠[-1.0, -ld_window_r2]⁠

Author(s)

Richèl J.C. Bilderbeek

See Also

use get_marker_correlation_coefficients_table to see the marker correlation coefficients between markers in a table

Examples

if (is_plink_installed()) {
  # Create example PLINK text data
  assoc_qt_data <- create_demo_assoc_qt_data()
  # PLINK checks for LD on markers on the same chromosome
  assoc_qt_data$data$map_table$CHR <- 1

  # PLINK uses a default value of ld_window_r2 = 0.2,
  # which, in this examples, does not give a result
  get_marker_correlation_coefficients(
    assoc_qt_data$data
  )

  # Show all values
  get_marker_correlation_coefficients(
    assoc_qt_data$data,
    ld_window_r2 = 0.0
  )

  # PLINK binary data
  assoc_qt_data$data <- convert_plink_text_data_to_plink_bin_data(
    assoc_qt_data$data
  )
  get_marker_correlation_coefficients(
    assoc_qt_data$data,
    ld_window_r2 = 0.0
  )
}

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