Phenotype simulation#

admix simulate-admix-pheno \
    --pfile <plink file prefix> \
    --hsq <heritability> \
    --cor <correlation> \
    --n-causal <number of causal SNPs> \
    --out-prefix <output prefix>

Parameter options#

admix.cli.simulate_admix_pheno(pfile: str, hsq: float, out_prefix: str, cor: float = 1.0, family: str = 'quant', n_causal: int | None = None, p_causal: float | None = None, case_prevalence: float = 0.5, seed: int | None = None, snp_effect: str | None = None, n_sim: int = 10)[source]#

Simulate phenotypes using a pgen file for admixed individuals.

Parameters:

  • pfile (str) – Path to the pgen file

  • hsq (float) – Heritability

  • out_prefix (str) – prefix to the output file, <out>.pheno, <out>.snpeffect will be created

  • cor (float) – genetic correlation across local ancestries

  • family (str) – phenotype type to simulate, either “quant” or “binary”

  • n_causal (int) – Number of causal variants to simulate

  • p_causal (float) – Proportion of a causal variant

  • case_prevalence (float) – Prevalence of cases, default 0.5

  • seed (int) – Random seed

  • beta (str) – Path to the beta file

  • n_sim (int) – Number of simulations to perform