simulate-pheno

Simulate a phenotype from real genotypes using additive, dominant, recessive, and interaction effects, following the liability-threshold model described in Concepts and methodology.

posthoc simulate-pheno

Usage

posthoc simulate-pheno [OPTIONS]

Options

--pfile <pfile>

Required Prefix of PLINK2 .pgen/.pvar/.psam fileset.

--additive <additive_terms>

Additive causal SNP: INDEX EFFECT_SIZE. Repeatable.

--dominant <dominant_terms>

Dominant causal SNP: INDEX EFFECT_SIZE. Repeatable.

--recessive <recessive_terms>

Recessive causal SNP: INDEX EFFECT_SIZE. Repeatable.

--interaction2 <interaction2_terms>

Two-way interaction: INDEX_I INDEX_J EFFECT_SIZE. Repeatable.

--interaction3 <interaction3_terms>

Three-way interaction: INDEX_I INDEX_J INDEX_K EFFECT_SIZE. Repeatable.

--logistic

Binary phenotype (case/control).

--linear

Continuous phenotype.

--heritability <heritability>

Fraction of liability variance from genotype.

--prevalence <prevalence>

Target case prevalence (logistic task only).

--recode-centered

Recode genotypes from 0/1/2 to -1/0/1 before simulating (Yelmen et al.).

--pheno-name <pheno_name>

Column name for the output phenotype.

--seed <seed>

--out <out_path>

Required Output phenotype file path.

Effect term encoding

• --additive INDEX EFFECT — contributes genotype * EFFECT to the liability, where genotype is the 0/1/2 allele count (or -1/0/1 if --recode-centered is set).

• --dominant INDEX EFFECT — contributes EFFECT only where the (centered) genotype equals -1; intended for use with --recode-centered.

• --recessive INDEX EFFECT — contributes EFFECT only where the (centered) genotype equals 1.

• --interaction2 INDEX_I INDEX_J EFFECT — contributes EFFECT * genotype_i * genotype_j.

• --interaction3 INDEX_I INDEX_J INDEX_K EFFECT — contributes EFFECT * genotype_i * genotype_j * genotype_k.

All five options are repeatable — pass --additive (or any other) more than once to add multiple independent terms. INDEX values are zero-based positions into the variant order of the --pfile, not variant IDs. At least one causal term must be given across all five options combined.

Exactly one of --logistic/--linear must be given. For --logistic, the liability is thresholded at the --prevalence quantile to produce a binary phenotype; for --linear, the liability itself (with noise scaled to hit the target --heritability) is the phenotype.

Outputs

See Output formats for the two files this command writes.