ABC_on_hyperparameters: Conduct an ABC on a range of effect size distribution...

In hemstrow/GeneArchEst: Estimate Genomic Architecture for Quantitative Traits

Conduct an ABC on a range of effect size distribution hyperparameters

Description

Runs Approximate Bayesian Computation across a range of marker effect size distribution hyperparameters by comparing the distributions of phenotypes produced to those in the real data.

Usage

ABC_on_hyperparameters(
  x,
  phenotypes,
  iters,
  effect_distribution = rbayesB,
  parameter_distributions = list(pi = function(x) rbeta(x, 25, 1), d.f = function(x)
    runif(x, 1, 100), scale = function(x) rbeta(x, 1, 3) * 100),
  h_dist = function(x) rep(0.5, x),
  center = TRUE,
  par = FALSE,
  phased = FALSE,
  save_effects = FALSE
)

Arguments

x	matrix. Input genotypes, SNPs as rows, columns as individuals. Genotypes formatted as 0,1,2 for the major homozygote, heterozygote, and minor homozygote, respectively.
phenotypes	numeric vector. Observed phenotypes, one per individual.
iters	numeric. Number of ABC permutations to run.
effect_distribution	function, default rbayesB. A function for a distribution of effect sizes. The first argument, n, should be the number of effects to draw. Other arguments must be named to match the names of the parameter distribution functions given in the parameter_distributions argument.
parameter_distributions	List containing named functions, defualt list(pi = function(x) rbeta(x, 25, 1), d.f = function(x) runif(x, 1, 100), scale = function(x) rbeta(x, 1, 3)*100). A list containing functions for each parameter in the effect size distribution. The given functions should be named to match the parameter for which they produce distributions, and should take a single argument, x, which holds the number of parameter values to draw.
h_dist	function, default function(x) rep(.5, x). A function for the distribution of heritability from which to draw h^2 values for each iteration. Must take a single argument, x, which holds the number of h values to draw. The default produces only heritabilities of .5.
center	logical, default T. Determines if the phenotypes provided and generated during each iteration should be centered (have their means set to 0).
par	numeric or FALSE, default FALSE. If numeric, the number of cores on which to run the ABC.

Details

Please note that no missing phenotypes or missing genotype data is permitted. Missing genotypes should be imputed (such as with impute_and_phase_beagle) before this function is run.

hemstrow/GeneArchEst documentation built on June 10, 2025, 5:06 a.m.