create_assoc_qt_params: Create parameters for the assoc_qt function

In richelbilderbeek/plinkr: Interface to PLINK

Create parameters for the assoc_qt function

Description

Create parameters to detect associations with quantitative traits (using assoc_qt). Use create_test_assoc_qt_params) to create a set of parameters that is used in testing.

Usage

create_assoc_qt_params(
  maf = get_lowest_maf(),
  confidence_interval = NA,
  allow_no_sex = FALSE,
  base_input_filename = file.path(get_plinkr_tempfilename(), "assoc_input"),
  base_output_filename = file.path(get_plinkr_tempfilename(), "assoc_output")
)

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

Value

the parameters to do a quantitative trait analysis

Note

This function is named after the --assoc PLINK flag, where --assoc uses phenotypic values to determine if an association is about a binary/case-control trait or a quantitative trait, plinkr uses functions named assoc and assoc_qt.

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_test_assoc_qt_params to create assoc_qt_params used for testing

Examples

create_assoc_qt_params()
create_assoc_qt_params(maf = 0.01)
create_assoc_qt_params(confidence_interval = 0.99)
create_assoc_qt_params(allow_no_sex = TRUE)

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