create_assoc_qt_args_on_plink_text_filenames: Internal function

In richelbilderbeek/plinkr: Interface to PLINK

Internal function

Description

Create the command-line arguments to call PLINK or PLINK2 to do a quantitative trait analysis, when PLINK text files are used as data

Usage

create_assoc_qt_args_on_plink_text_filenames(
  assoc_qt_data,
  assoc_qt_params,
  plink_options = create_plink_options()
)

Arguments

assoc_qt_data	data use to used by assoc_qt (as created by create_assoc_qt_data), which equals 'regular' data (see check_data) and a phenotype table/file
assoc_qt_params	parameters to do an association analysis for a quantitative trait (i.e. using assoc_qt), as can be created by create_assoc_qt_params
plink_options	options to run PLINK, as created by create_plink_options

Value

the command-line arguments

Author(s)

Richèl J.C. Bilderbeek

See Also

see create_assoc_qt_args for all the specialized functions to create the PLINK/PLINK2 command-line arguments

Examples

assoc_qt_data <- create_assoc_qt_data(
  data = create_plink_text_filenames(
    map_filename = get_plinkr_filename("demo_assoc_qt.map"),
    ped_filename = get_plinkr_filename("demo_assoc_qt.ped")
  ),
  phenotype_data = create_test_phenotype_data_filename(
    phe_filename = get_plinkr_filename("demo_assoc_qt.phe")
  )
)
create_assoc_qt_args_on_plink_text_filenames(
  assoc_qt_data = assoc_qt_data,
  assoc_qt_params = create_test_assoc_qt_params()
)

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