gscramble

gscramble simulates admixed individuals without replacement to address spurious power inflation in genetic clustering algorithms.

Key Features:

• Pedigree specification: Users can specify pedigrees of varying complexity to simulate admixed genotypes.
• Haplotype block tracking: The package segregates and tracks haplotype blocks from different source populations through specified pedigrees.
• Without-replacement sampling: Alleles are sampled from empirical data without replacement to avoid resampling-induced, spurious power inflation (RISPI).
• Recombination rate integration: Alleles are segregated based on species-specific recombination rates to respect physical linkage between markers on the same chromosome.
• Permutation schemes: Multiple permutation schemes are available for sampling alleles from empirical data into haplotype blocks.

Scientific Applications:

• Genetic clustering algorithm evaluation: Provides simulated data for parallel analyses to evaluate the behavior of genetic clustering algorithms on empirical data.
• Admixture simulation: Enables simulation of biologically informed individual genotypes from empirical data for admixture studies.
• Linkage-aware simulation: Supports simulation that respects physical linkage between markers on the same chromosome.

Methodology:

gscramble allows users to specify pedigrees, then segregates and tracks haplotype blocks from different source populations through those pedigrees, and samples alleles from empirical data into those haplotype blocks using a variety of permutation schemes, without replacement and based on species-specific recombination rates.