simulate_null_haplotypes: A function for generating fake data

In jeinson/tompen: [Sta]tistics for [M]odified [Pen]etrance

A function for generating fake data

Description

This function can simulate some haplotype combinations based on allele frequencies sampled from beta distributions. The qtl frequencies are assumed to represent the higher expressed allele. qtl frequencies are drawn from a beta distribution, defined by the parameters 'qtl_alpha' and 'qtl_beta'

Usage

simulate_null_haplotypes(
  n_indvs,
  n_genes,
  c_alpha = 0.656,
  c_beta = 437.47,
  qtl_alpha = 1,
  qtl_beta = 1,
  maf_cutoff = 0.05
)

Arguments

n_indvs	The number of individuals to simulate
n_genes	The number of genes to simulate
c_alpha	shape parameter for the csnp allele frequency. Default = 4
c_beta	shape parameter beta for the csnp allele frequency. Default = 3000
qtl_alpha	shape parameter alpha for the qtl allele frequency. Default = 1
qtl_beta	shape paramteter beta for the qtl allele frequency. Default = 1
maf_cutoff	cutoff for the minimum qtl allele frequency when simulating data. This will force the beta distribution for the qtl allele frequency to these limits.

Examples

simulate_null_haplotypes(n_indvs = 100, n_genes = 5)

jeinson/tompen documentation built on March 18, 2023, 2:59 a.m.