create_assoc_qt_covar_params: Create parameters for the assoc_qt_covar function

In richelbilderbeek/plinkr: Interface to PLINK

Create parameters for the assoc_qt_covar function

Description

Create parameters to detect associations with quantitative traits and covariates (using assoc_qt_covar). Use create_test_assoc_qt_covar_params) to create a set of parameters that is used in testing.

Usage

create_assoc_qt_covar_params(
  maf = get_lowest_maf(),
  confidence_interval = 0.95,
  allow_no_sex = FALSE,
  base_input_filename = file.path(get_plinkr_tempfilename(), "assoc_qt_covar_input"),
  base_output_filename = file.path(get_plinkr_tempfilename(), "assoc_qt_covar_input")
)

Arguments

maf	minor allele frequency threshold. Alleles that have a frequency lower than the MAF are excluded from the PLINK analysis. maf must be a value between zero and 0.5 (i.e. excluding zero and excluding 0.5). By default, maf is set to the lowest representable non-zero floating-point value, as obtained by get_lowest_maf The parameter name maf is named after the PLINK --maf flag. This was chosen over more specific names such as min_allele_frequency).
confidence_interval	confidence interval, a value between (and excluding both) 0.0 and 1.0. The confidence interval helps assess the certainty of an estimation: you can be 99 percent sure a value is within the range of the 0.99 confidence interval The confidence_interval is only used by PLINK2. For PLINK, its value is ignored
allow_no_sex	set this to TRUE to retain phenotype values for missing-sex samples. This parameter is named after the PLINK --allow-no-sex flag
base_input_filename	the base of the filenames that are used as input for PLINK/PLINK2
base_output_filename	the base of the filenames that are used as output for PLINK/PLINK2

Note

This function is named after the --assoc and --covar PLINK flags, as well as forcing PLINK to use quantitative trait phenotypic values.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_assoc_qt_covar_params(create_assoc_qt_covar_params())
check_assoc_qt_covar_params(create_test_assoc_qt_covar_params())

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