convert_plink_text_data_to_plink2_bin_data: Convert the 'PLINK' text data to 'PLINK' binary data

In richelbilderbeek/plinkr: Interface to PLINK

Convert the PLINK text data to PLINK binary data

Description

Convert the PLINK text data to PLINK binary data.

Usage

convert_plink_text_data_to_plink2_bin_data(
  plink_text_data,
  base_output_plink1_filename = plinkr::get_plinkr_tempfilename(fileext = ""),
  base_output_plink2_filename = plinkr::get_plinkr_tempfilename(fileext = ""),
  plink1_options = create_plink_v1_9_options(),
  plink2_options = create_plink_v2_0_options(),
  verbose = FALSE
)

Arguments

plink_text_data	the genetic and phenotypic data for PLINK to work on, in PLINK text format, as created by create_plink_text_data.
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.

Value

the same list that was used as input, except that the following elements

• ped_table (see check_ped_table)

• map_table (see check_map_table)

are replaced by:

• pgen_table (see check_pgen_table)

• psam_table (see check_psam_table)

• pvar_table (see check_pvar_table)

The other list elements are left as-is.

Author(s)

Richèl J.C. Bilderbeek

See Also

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

• To convert from PLINK1 text data

  • to PLINK1 binary data: use convert_plink_text_data_to_plink_bin_data

  • to PLINK2 binary data, use convert_plink_text_data_to_plink2_bin_data

• To convert from PLINK1 binary data

  • to PLINK text data, use convert_plink_bin_data_to_plink_text_data

  • to PLINK2 binary data, use convert_plink_bin_data_to_plink2_bin_data

• To convert from PLINK2 binary data

  • to PLINK text data, use convert_plink2_bin_data_to_plink_text_data

  • to PLINK binary data, use convert_plink2_bin_data_to_plink_bin_data

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