danwkenn/SimAdmixtR: Simulates a set of admixed diploid genotypes based on SNP allele frequencies

The package imports the SNP allele frequencies from two or more origin populations, as well as the number and make-up of ancestors. It then randomly samples the ancestor genomes from the origin populations, and then, using Mendelian rules, simulates the inheritance of alleles down to the current generation. It can also repeat this process a specified number of times. The package then outputs the set of repeated simulated genotypes as text file in the input format of the STRUCTURE program. The simulation method makes some significant assumptions, and one should be careful to ensure that these assumptions are consistent with reality before using these simulations in analyses. First, it is assumed the uncertainty in the ancestor population allele frequencies are accurate with negligible uncertainty for the context of the analyis. Secondly, it is assumed that all SNP inheritance probabilities are statistically independent and subject to Hardy-Weinberg Equilibrium conditions with regards genotype. Therefore, situations of linkage disequilibrium or significant selection pressure cannot be simulated using this tool. Thirdly, it is assumed that all SNPs are located on autosomal pairs. SNPs on sex chromosomes have a different inheritance properties, and thus cannot be simulated using this tool. Finally, it is assumed that the mutation rate is of DNA is negligible. While this will generally be true, if the tool is used for many thousands of SNPs for many generations, even a very low mutation rate per site per generation could become relevant.

install.packages("remotes")
remotes::install_github("danwkenn/SimAdmixtR")