scripts/create_inst_ext_example_files.R

In richelbilderbeek/plinkr: Interface to PLINK

# Create the example files in the inst/extdata folder
set.seed(314)
assoc_data <- create_demo_assoc_data()
save_map_table(
  map_table = assoc_params$data$map_table,
  file.path(system.file("extdata", package = "plinkr"), "demo_assoc.map")
)
save_ped_table(
  ped_table = assoc_params$data$ped_table,
  file.path(system.file("extdata", package = "plinkr"), "demo_assoc.ped")
)

set.seed(314)
assoc_qt_params <- create_demo_assoc_qt_data()
save_map_table(
  map_table = assoc_qt_data$data$map_table,
  file.path(system.file("extdata", package = "plinkr"), "demo_assoc_qt.map")
)
save_ped_table(
  ped_table = assoc_qt_data$data$ped_table,
  file.path(system.file("extdata", package = "plinkr"), "demo_assoc_qt.ped")
)
save_phe_table(
  phe_table = assoc_qt_params$phe_table,
  phe_filename = file.path(system.file("extdata", package = "plinkr"), "demo_assoc_qt.phe")
)

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")
)