simplePHENOTYPES

simplePHENOTYPES simulates pleiotropic, linked, and epistatic phenotypes across diverse genetic architectures to support validation of multivariate statistical methods in genomics.

Key Features:

• High-throughput simulation: Simulates thousands of phenotypes rapidly, typically in less than one minute.
• Genetic models: Supports additive, dominance, and epistatic genetic models.
• Pleiotropy and correlations: Generates complete pleiotropy, partial pleiotropy, spurious pleiotropy, and correlated traits.
• Input format compatibility: Accepts HapMap, VCF, GDS, and Plink bed/ped files as well as numeric datasets via file paths or matrices.
• Integration with GWAS software: Produces outputs compatible with standard Genome-Wide Association Studies (GWAS) software and ensures numerical equivalence of simulated phenotypes to other packages.

Scientific Applications:

• Validation of multivariate methods: Testing and validation of multivariate statistical approaches using simulated realistic genetic data.
• Assessment of GWAS and GS methods: Rigorous assessment of statistical methods in Genome-Wide Association Studies (GWAS) and Genomic Selection (GS).

Methodology:

Implements simulation of additive, dominance, and epistatic genetic models; generates complete, partial, and spurious pleiotropy and correlated traits; accepts genotype inputs in HapMap, VCF, GDS, and Plink bed/ped formats or numeric matrices; and produces numerically equivalent phenotypes for comparison with other packages.