Simulate genetic data — gen

This function is used to simulate genetic data. Using parallelization the function can simulate genotypes, liabilities both with and without family structure. The function will return a list where all information about the simulation can be found. This includes which SNP are casual and what their effect is, the genetic and full liabilities og subjects, parents and siblings and their phenotypes. This object can be used to further develop or test statistical analysis on genetic data.

Usage

gen_sim(
  filename,
  beta = NULL,
  MAF = NULL,
  N = 1e+05,
  M = 1e+05,
  n_sib = 0,
  K = 0.05,
  h2 = 0.5,
  C = 1000,
  block_size = 1000,
  fam = TRUE,
  parallel_plan = "multisession"
)

Arguments

filename: Filename for file backed matrix(FBM) and rds file.
beta: Vector containing casual effect of each SNP. If NULL a vector will be simulated.
MAF: Vector containing minor allele frequencies (MAF). If NULL a vector will be simulated.
N: Amount of subjects.
M: Amount of SNPs.
K: The prevalance of trait.
h2: The heritability of trait.
C: Amount of causal SNP's.
block_size: Size of FBM to be processed in each iteration.
fam: Boolean deciding if simulation should include a family structure.
parallel_plan: Plan for parallelization. See ?future::plan.
n_sibs: Amount of siblings.

Value

rds file referring to a list containing FBM with genotypes, generated SNP info and information about subject and family.