In richelbilderbeek/plinkr: Interface to PLINK

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

This vignette shows how to plinkr example files were created.

library(plinkr)

Methods

To demonstrate how the plinkr example files were created, these are re-created in a temporary folder, and then compared to the existing files in the plinkr inst/extdata folder

Determine the name of the temporary folder:

folder_name <- plinkr::get_plinkr_tempfilename()
folder_name

`demo_assoc`

Simulate data:

# Create the example files in the inst/extdata folder
set.seed(314)
assoc_data <- create_demo_assoc_data()

Glance at the data:

knitr::kable(assoc_data$data$map_table)

knitr::kable(assoc_data$data$ped_table)

Should be the same:

testthat::expect_equal(
  assoc_data$data$map_table,
  read_plink_map_file(get_plinkr_filename("demo_assoc.map"))
)

testthat::expect_equal(
  assoc_data$data$ped_table,
  read_plink_ped_file(get_plinkr_filename("demo_assoc.ped"))
)

`demo_assoc_qt`

plain-text files

set.seed(314)
assoc_qt_data <- create_demo_assoc_qt_data()

Glance at the data:

knitr::kable(assoc_qt_data$data$map_table)

knitr::kable(assoc_qt_data$data$ped_table)

knitr::kable(assoc_qt_data$phenotype_data$phe_table)

Should be equal:

testthat::expect_equal(
  assoc_qt_data$data$map_table,
  read_plink_map_file(get_plinkr_filename("demo_assoc_qt.map"))
)

testthat::expect_equal(
  assoc_qt_data$data$ped_table,
  read_plink_ped_file(get_plinkr_filename("demo_assoc_qt.ped"))
)

if (1 == 2) {
  plinkr::save_phe_table(
    phe_table = assoc_qt_params$phe_table,
    phe_filename = get_plinkr_filename("demo_assoc_qt.phe")
  )
  testthat::expect_equal(
    assoc_qt_params$phe_table,
    read_plink_phe_file(get_plinkr_filename("demo_assoc_qt.phe"))
  )
}

binary files

if (1 == 2) {
  make_bed(
    base_input_filename = file.path(
      system.file("extdata", package = "plinkr"), "demo_assoc_qt"
    ),
    base_output_filename = file.path(
      system.file("extdata", package = "plinkr"), "demo_assoc_qt"
    )
  )

  make_bed(
    base_input_filename = file.path(
      system.file("extdata", package = "plinkr"), "demo_assoc"
    ),
    base_output_filename = file.path(
      system.file("extdata", package = "plinkr"), "demo_assoc"
    )
  )
}