assoc_qt: Let 'PLINK'/'PLINK2' detect an association with one or more...

In richelbilderbeek/plinkr: Interface to PLINK

Let PLINK/PLINK2 detect an association with one or more quantitative traits.

Description

Let PLINK/PLINK2 detect an association with one or more quantitative traits.

Usage

assoc_qt(
  assoc_qt_data,
  assoc_qt_params = create_assoc_qt_params(),
  plink_options = create_plink_options(),
  verbose = FALSE
)

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
verbose	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Value

A assoc_qt_result, which is a list which is a list with elements:

• qassoc_table: the quantitative analysis results table, as can be checked by check_qassoc_table

• log: the text from the log file created by PLINK/PLINK2 when doing assoc_qt

Note

This function is named after the --assoc flag used by PLINK.

Author(s)

Richèl J.C. Bilderbeek

See Also

Use assoc to do a case-control association

Examples

if (is_plink_installed()) {
  # Demo data
  assoc_qt(
    assoc_qt_data = create_demo_assoc_qt_data(),
    assoc_qt_params = create_test_assoc_qt_params()
  )
}

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