assoc_qt_covar: Let PLINK detect an association with one ore more...

In richelbilderbeek/plinkr: Interface to PLINK

Let PLINK detect an association with one ore more quantitative traits.

Description

Let PLINK detect an association with one ore more quantitative traits.

Usage

assoc_qt_covar(
  assoc_qt_covar_data,
  assoc_qt_covar_params,
  plink_options = create_plink_options(),
  verbose = FALSE
)

Arguments

assoc_qt_covar_data	data to do an association analysis for a quantitative trait with covariates (i.e. using assoc_qt_covar), as can be created by create_assoc_qt_covar_data
assoc_qt_covar_params	parameters to do an association analysis for a quantitative trait with covariates (i.e. using assoc_qt_covar), as can be created by create_assoc_qt_covar_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 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

The table with have as much rows as the number of SNPs multiplied by the number of traits.

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

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