Simulate a genomic prediction dataset — simulate

Generates a small marker matrix and a phenotype with a known narrow-sense heritability, for examples, tests and demonstrations. Markers are coded as allele dosages (0, 1, 2). A random subset of markers are QTL with additive effects; the phenotype is the resulting breeding value plus normal noise scaled to the target heritability.

Usage

simulate_population(n = 200, m = 1000, n_qtl = 50, h2 = 0.5, seed = NULL)

Arguments

n: Number of individuals. Default 200.
m: Number of markers. Default 1000.
n_qtl: Number of markers with a non-zero (QTL) effect. Default 50.
h2: Target narrow-sense heritability in (0, 1]. Default 0.5.
seed: Optional integer seed for reproducibility. Applied with withr::with_seed(), which scopes the seed locally and leaves the caller's random-number state unchanged.

Value

A list with geno (an n x m 0/1/2 matrix, row/column names set), pheno (length-n numeric), bv (true breeding values), qtl (indices of the causal markers) and h2 (the realised heritability).

Examples

sim <- simulate_population(n = 100, m = 300, seed = 1)
dim(sim$geno)
#> [1] 100 300
length(sim$pheno)
#> [1] 100