Simulating Admixed Genotypes Without Replacement

A genomic simulation approach for creating biologically informed individual genotypes from empirical data that 1) samples alleles from populations without replacement, 2) segregates alleles based on species-specific recombination rates. 'gscramble' is a flexible simulation approach that allows users to create pedigrees of varying complexity in order to simulate admixed genotypes. Furthermore, it allows users to track haplotype blocks from the source populations through the pedigrees.

gscramble

This is an R package for simulating individuals that are admixed between different populations according to a pedigree. To do so it uses sampling without replacement from samples taken from each population.

You can read the documentation for it at: https://eriqande.github.io/gscramble/

You can install in from GitHub:

remotes::install_github(
  "eriqande/gscramble", 
  build_opts = c("--no-resave-data"), 
  build_vignettes = TRUE, 
  build_manual = TRUE,
  quiet = FALSE
)

Once that is installed you can read the vignettes:

vignette("gscramble-tutorial")  # information on input data objects
vignette("about-createGSP")  # a function to make simple genomic simulation pedigrees
vignette("permutation-options")  # about the different options for permuting