set.params: Set parameters

In jendelman/GWASpoly: Genome-wide Association Studies for Autopolyploids

Set parameters

Description

Set parameters

Usage

set.params(
  fixed = NULL,
  fixed.type = NULL,
  n.PC = 0,
  MAF = NULL,
  geno.freq = NULL,
  P3D = TRUE
)

Arguments

fixed	Vector of names of fixed effects
fixed.type	Vector of effect types ("numeric" or "factor"), corresponding to the effects listed in "fixed"
n.PC	Number of principal components to include as covariates
MAF	Minimum minor allele frequency
geno.freq	Maximum genotype frequency (after applying dominance relations)
P3D	TRUE/FALSE whether to use the P3D approximation (variance components not re-estimated for every marker)

Details

The list returned by the function should be passed to GWASpoly function.

Value

A list with the following components

fixed	Names of fixed effects
fixed.type	Types of fixed effects
n.PC	Number of principal components to include as covariates
min.MAF	Minimum minor allele frequency
max.geno.freq	Maximum genotype frequency (after applying dominance relations)
P3D	TRUE/FALSE whether to use the P3D approximation

jendelman/GWASpoly documentation built on Oct. 16, 2024, 5:59 a.m.