mgp_simulate

Simulate Complex Traits (mgp_simulate)

mgp_simulate simulates quantitative or case-control phenotypes from PLINK BED genotype data using magenpy's phenotype simulation machinery.

mgp_simulate --help

Basic Usage

mgp_simulate \
  --bfile data/chr_22 \
  --h2 0.5 \
  --prop-causal 0.1 \
  --output-file output/pheno_1

This writes output/pheno_1.SimPheno. Add --output-simulated-beta to also write output/pheno_1.SimEffect.

Genetic Architecture

For a simple spike-and-slab architecture, use --prop-causal:

mgp_simulate --bfile data/chr_22 --h2 0.5 --prop-causal 0.05 --output-file output/pheno

For custom mixture proportions and variance multipliers, use --mix-prop with --var-mult:

mgp_simulate \
  --bfile data/chr_22 \
  --h2 0.5 \
  --mix-prop 0.9,0.1 \
  --var-mult 0,1 \
  --output-file output/pheno

Case-Control Traits

mgp_simulate \
  --bfile data/chr_22 \
  --h2 0.3 \
  --phenotype-likelihood binomial \
  --prevalence 0.08 \
  --output-file output/case_control

Use --log-level to control command-line logging.