assoc_qt_on_plink_text_data: Let PLINK detect an association with one or more quantitative...

In richelbilderbeek/plinkr: Interface to PLINK

Let PLINK detect an association with one or more quantitative traits with data in PLINK text format.

Description

Let PLINK detect an association with one or more quantitative traits. with data in PLINK text format.

Usage

assoc_qt_on_plink_text_data(
  assoc_qt_data,
  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 tibble with the detected associations. The table with have as much rows as the number of SNPs multiplied by the number of traits.

If the assoc_qt_params used PLINK1 text or PLINK1 binary data, the tibble has the following columns:

• trait_name: name of the quantitive trait, taken from the phenotype table column name

• CHR: Chromosome number

• SNP: SNP identifier

• BP: Physical position (base-pair)

• NMISS: Number of non-missing genotypes

• BETA: Regression coefficient

• SE: Standard error

• R2: Regression r-squared

• T: Wald test (based on t-distribution)

• P: Wald test asymptotic p-value

Note that parameters in uppercase are named as such by PLINK.

Note

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

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_plink_installed()) {
  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.