convert_plink_text_files_to_plink2_bin_files: Convert 'PLINK' text data files to 'PLINK2' binary data files

In richelbilderbeek/plinkr: Interface to PLINK

Convert PLINK text data files to PLINK2 binary data files

Description

Convert PLINK text data files to PLINK2 binary data files, by

Usage

convert_plink_text_files_to_plink2_bin_files(
  base_input_filename,
  base_output_plink1_filename = file.path(dirname(base_input_filename),
    "output_plink1"),
  base_output_plink2_filename = file.path(dirname(base_input_filename),
    "output_plink2"),
  plink1_options = create_plink_v1_9_options(),
  plink2_options = create_plink_v2_0_options(),
  verbose = FALSE
)

Arguments

base_input_filename	the base of the filenames that are used as input for PLINK/PLINK2
base_output_plink1_filename	temporary folder to create the PLINK binary files in
base_output_plink2_filename	temporary folder to create the PLINK2 binary files in
plink1_options	the PLINK version, as created by create_plink_options, for any version of PLINK
plink2_options	the PLINK2 version, as created by create_plink_options, for any version of PLINK2
verbose	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Details

1. convert PLINK text data files to PLINK binary data files, using convert_plink_text_files_to_plink_bin_files, with base_output_plink1_filename as a temporary folder and plink1_options as the PLINK version

2. convert PLINK binary data files to PLINK2 binary data files, using convert_plink_bin_files_to_plink2_bin_files with base_output_plink2_filename as a temporary folder and plink2_options as the PLINK2 version

Value

a list with the following elements:

• pgen_filename: the full .pgen filename

• psam_filename: the full .psam filename

• pvar_filename: the full .pvar filename

• log_filename: the full .log filename

Author(s)

Richèl J.C. Bilderbeek

See Also

these are the functions to convert between the PLINK and PLINK2 files:

• To convert from PLINK1 text files

  • to PLINK1 binary files: use convert_plink_text_files_to_plink_bin_files

  • to PLINK2 binary files, use convert_plink_text_files_to_plink2_bin_files

• To convert from PLINK1 binary files

  • to PLINK text files, use convert_plink_bin_files_to_plink_text_files

  • to PLINK2 binary files, use convert_plink_bin_files_to_plink2_bin_files

• To convert from PLINK2 binary files

  • to PLINK text files, use convert_plink2_bin_files_to_plink_text_files

  • to PLINK binary files, use convert_plink2_bin_files_to_plink_bin_files

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