read_gcae_input_files: Read the GenoCAE input filenames

In richelbilderbeek/gcaer: Interface to GCAE

Read the GenoCAE input filenames

Description

Read the GenoCAE input filenames

Usage

read_gcae_input_files(gcae_input_filenames, verbose = TRUE)

Arguments

gcae_input_filenames

the GCAE input filenames, in the form of a list with the following elements: bed_filename: path to a .bed file, as can be read by read_plink_bed_file bim_filename: path to a .bim file, as can be read by read_plink_bim_file fam_filename: path to a .fam file, as can be read by read_plink_fam_file phe_filename: path to a .phe file, as can be read by read_plink_phe_file labels_filename: path to a .csv file as can be read by read_labels_file

verbose

the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Value

the GCAE data in the form of a list with the following elements:

• bed_table: a .bed table, as can be checked by check_bed_table

• bim_table: a .bim table, as can be checked by check_bim_table

• fam_table: a .fam table, as can be checked by check_fam_table

• phe_table: a .phe table, as can be checked by check_phe_table

• labels_table: a .csv table, as can be checked by check_labels_table

Author(s)

Richèl J.C. Bilderbeek

Examples

if (plinkr::is_plink_installed()) {
  # Create the files
  gcae_input_filenames <- create_gcae_input_files_1(
    base_input_filename = get_gcaer_tempfilename()
  )

  # Read the files
  gcae_input_data <- read_gcae_input_files(gcae_input_filenames)

  # Summarise the data
  summarise_gcae_input_data(gcae_input_data)

  # Clean up
  file.remove(as.character(unlist(gcae_input_filenames)))
}

richelbilderbeek/gcaer documentation built on March 25, 2024, 3:08 p.m.