Skip to contents

Simulate Quantitative Traits from PLINK Genotypes

Source: R/simulate_traits.R
simulate_traits.Rd

This function simulates a quantitative trait based on additive and epistatic genetic effects using genotype data from a PLINK dataset. The simulated trait is saved to a specified output file in a phenotype format compatible with PLINK.

Usage

simulate_traits(
  plink_file,
  output_file,
  additive_heritability,
  gxg_heritability,
  additive_indices,
  gxg_indices_1,
  gxg_indices_2,
  log_level = "WARNING"
)

Arguments

Character. Path to the PLINK dataset (without file extension). The function will append .bed, .bim, and .fam extensions as needed.

output_file

Character. Path to the output file where the simulated trait will be saved.

additive_heritability

Numeric. A value between 0 and 1 specifying the proportion of trait variance due to additive genetic effects.

gxg_heritability

Numeric. A value between 0 and 1 specifying the proportion of trait variance due to gene-by-gene (epistatic) interactions. The sum of additive_heritability and gxg_heritability must not exceed 1.

additive_indices

Integer vector. Indices of SNPs contributing to additive genetic effects.

gxg_indices_1

Integer vector. Indices of SNPs in the first group for epistatic interactions.

gxg_indices_2

Integer vector. Indices of SNPs in the second group for epistatic interactions.

log_level

Character. Logging level for messages (e.g., "DEBUG", "INFO", "WARNING"). Default is "WARNING".

Value

None. The simulated trait is written to the specified output_file.

Details

The function uses the following components to simulate the trait:

  • Additive genetic effects: Determined by additive_indices and the specified additive_heritability.

  • Epistatic interactions: Simulated using pairs of SNPs from gxg_indices_1 and gxg_indices_2, contributing to the gxg_heritability.

  • Environmental effects: Any remaining variance not explained by genetic effects is assigned to random environmental noise.

The output file is in PLINK-compatible phenotype format with three columns: Family ID (FID), Individual ID (IID), and the simulated trait (TRAIT).

Examples

plink_file <- gsub("\\.bed", "", system.file("testdata", "test.bed", package = "smer"))
out_file <- tempfile()
additive_heritability <- 0.3
gxg_heritability <- 0.1
additive_snps <- sort(sample(1:100, 50, replace = FALSE))
gxg_group_1 <- sort(sample(additive_snps, 10, replace = FALSE))
gxg_group_2 <- sort(sample(setdiff(additive_snps, gxg_group_1), 10, replace = FALSE))
n_samples <- 200
simulate_traits(
  plink_file,
  out_file,
  additive_heritability,
  gxg_heritability,
  additive_snps,
  gxg_group_1,
  gxg_group_2
)
from_file <- read.table(out_file, header = TRUE)
head(from_file)
#>   FID IID       TRAIT
#> 1   1   1  0.07327543
#> 2   2   1 -0.82216034
#> 3   3   1 -2.31319310
#> 4   4   1  0.74270008
#> 5   5   1 -2.53693229
#> 6   6   1  1.26249797