create_assoc_qt_args: Create the command-line arguments to call 'PLINK' or 'PLINK2'...

In richelbilderbeek/plinkr: Interface to PLINK

Create the command-line arguments to call PLINK or PLINK2 to do a quantitative trait analysis, depending on the type of data.

Description

Create the command-line arguments to call PLINK or PLINK2 to do a quantitative trait analysis, depending on the type of data.

Usage

create_assoc_qt_args(
  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

These are the specialized functions:

• create_assoc_qt_args_on_plink_text_data

• create_assoc_qt_args_on_plink_bin_data

• create_assoc_qt_args_on_plink2_bin_data

• create_assoc_qt_args_on_plink_text_filenames

• create_assoc_qt_args_on_plink_bin_filenames

• create_assoc_qt_args_on_plink2_bin_filenames

Examples

create_assoc_qt_args(
  assoc_qt_data = create_test_assoc_qt_data(),
  assoc_qt_params = create_test_assoc_qt_params(),
  plink_options = create_plink_options()
)

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