## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  message = FALSE,
  warning = FALSE
)

## ----setup--------------------------------------------------------------------
library(smer)
library(genio)

## ----genotypes, eval=FALSE----------------------------------------------------
# plink_file <- tempfile()
# n_samples <- 3000
# n_snps <- 5000
# maf <- 0.05 + 0.45 * runif(n_snps)
# random_minor_allele_counts   <- (runif(n_samples * n_snps) < maf) +
#                                 (runif(n_samples * n_snps) < maf)
# allele_count_matrix <- matrix(random_minor_allele_counts,
#   nrow = n_samples,
#   ncol = n_snps,
#   byrow = TRUE,
# )
# 
# # Create .fam and .bim data frames
# fam <- data.frame(
#   fam = sprintf("F%d", 1:n_samples),       # Family ID
#   id = sprintf("I%d", 1:n_samples),       # Individual ID
#   pat = 0,                        # Paternal ID
#   mat = 0,                        # Maternal ID
#   sex = sample(1:2, n_samples, replace = TRUE),
#   pheno = -9
# )
# 
# bim <- data.frame(
#   chr = 1,               # Chromosome number
#   id = sprintf("rs%d", 1:n_snps),   # SNP name
#   posg = 0,                         # Genetic distance (cM)
#   pos = 1:n_snps,          # Base-pair position
#   ref = sample(c("A", "C", "G", "T"), n_snps, replace = T), # Minor allele
#   alt = sample(c("A", "C", "G", "T"), n_snps, replace = T)  # Major allele
# )
# 
# # Write to .bed, .fam, and .bim files
# write_plink(
#   file = plink_file,
#   X = t(allele_count_matrix),
#   fam = fam,
#   bim = bim
# )

## ----traits, eval=FALSE-------------------------------------------------------
# pheno_file <- tempfile()
# additive_heritability <- 0.3
# gxg_heritability <- 0.25
# n_snps_gxg_group <- 5
# n_snps_additive <- 100
# additive_snps <- sort(sample(1:n_snps, n_snps_additive, replace = F))
# gxg_group_1 <- sort(sample(additive_snps, n_snps_gxg_group, replace = F))
# gxg_group_2 <- sort(sample(setdiff(additive_snps, gxg_group_1),
#                            n_snps_gxg_group, replace = F))
# 
# simulate_traits(
#   plink_file,
#   pheno_file,
#   additive_heritability,
#   gxg_heritability,
#   additive_snps,
#   gxg_group_1,
#   gxg_group_2
# )

## ----seesionInfo--------------------------------------------------------------
sessionInfo()