data-raw/simulate_epistasis.R

In lcrawlab/mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test

library(dplyr)
library(mvMAPIT) # install mvMAPIT prior to running this file
set.seed(1234)

n_samples <- 500
n_snp <- 1000

sample_names <- seq_len(n_samples) %>% sprintf(fmt = "id%04d")
snp_names <- seq_len(n_snp) %>% sprintf(fmt = "snp%04d")

random_genotype_vec <- sample(0:2, n_samples * n_snp, replace = TRUE)
genotype_data <- matrix(random_genotype_vec,
  nrow = n_samples,
  ncol = n_snp,
)

colnames(genotype_data) <- snp_names
rownames(genotype_data) <- sample_names

seed <- 67132
d <- 2
PVE <- 0.8
rho <- 0.2
n_causal <- 200
n_trait_specific <- 0
n_pleiotropic <- 5
group_ratio_pleiotropic <- 1
epistatic_correlation <- 0.9
maf <- 0.05
simulated_data <- simulate_traits(
    genotype_data,
    n_causal = n_causal,
    n_trait_specific = n_trait_specific,
    n_pleiotropic = n_pleiotropic,
    d = d,
    H2 = PVE,
    rho = rho,
    epistatic_correlation = epistatic_correlation,
    group_ratio_pleiotropic = group_ratio_pleiotropic,
    maf_threshold = maf,
    seed = seed,
    logLevel = "ERROR"
)
usethis::use_data(simulated_data, overwrite = TRUE)