save_plink_text_data: Save 'PLINK' text data to files.

In richelbilderbeek/plinkr: Interface to PLINK

Save PLINK text data to files.

Description

Save PLINK text data to files.

Usage

save_plink_text_data(
  plink_text_data,
  base_input_filename = get_plinkr_tempfilename(),
  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_input_filename	the base of the filenames that are used as input for PLINK/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 full paths to the .bed, .bim and .fam files created

Author(s)

Richèl J.C. Bilderbeek

See Also

to save PLINK/PLINK2 data use:

• save_plink_text_data: to save PLINK text data

• save_plink_bin_data: to save PLINK binary data

• save_plink2_bin_data: to save PLINK2 binary data

Examples

#
# Example 1: using plinkr::create_test_plink_text_data
#

# Folder and base filename to save to
base_input_filename <- file.path(
  get_plinkr_tempfilename(),
  "save_plink_text_data"
)

# Create PLINK text data
plink_text_data <- create_test_plink_text_data()

# Save. Convenient: filenames are returned!
plink_text_filenames <- save_plink_text_data(
  plink_text_data = plink_text_data,
  base_input_filename = base_input_filename
)

# Cleanup
file.remove(plink_text_filenames$map_filename)
file.remove(plink_text_filenames$ped_filename)
unlink(dirname(base_input_filename), recursive = TRUE)

#
# Example 2: using plinkr::create_demo_assoc_qt_data
#

# Folder and base filename to save to
base_input_filename <- file.path(
  get_plinkr_tempfilename(),
  "save_plink_text_with_demo_assoc_qt_data"
)

# Create PLINK text data
assoc_qt_data <- create_demo_assoc_qt_data()

# Save. Convenient: filenames are returned!
plink_text_filenames <- save_plink_text_data(
  plink_text_data = create_test_plink_text_data(),
  base_input_filename = base_input_filename
)

# Cleanup
file.remove(plink_text_filenames$map_filename)
file.remove(plink_text_filenames$ped_filename)
unlink(dirname(base_input_filename), recursive = TRUE)

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