A package for modeling and simulating an admixed population
The underlying model is called the BN-PSD admixture model, which combines the Balding-Nichols (BN) allele frequency model for the intermediate subpopulations with the Pritchard-Stephens-Donnelly (PSD) model of individual-specific admixture proportions. The BN-PSD model enables the simulation of complex population structures, ideal for illustrating challenges in kinship coefficient and FST estimation. Simulated loci are drawn independently (in linkage equilibrium).
Maintainer: Alejandro Ochoa alejandro.ochoa@duke.edu (ORCID)
Authors:
John D. Storey jstorey@princeton.edu (ORCID)
Useful links:
# dimensions of data/model # number of loci m_loci <- 10 # number of individuals n_ind <- 5 # number of intermediate subpops k_subpops <- 2 # define population structure # FST values for k = 2 subpopulations inbr_subpops <- c(0.1, 0.3) # admixture proportions from 1D geography admix_proportions <- admix_prop_1d_linear(n_ind, k_subpops, sigma = 1) # also available: # - admix_prop_1d_circular # - admix_prop_indep_subpops # get pop structure parameters of the admixed individuals # the coancestry matrix coancestry <- coanc_admix(admix_proportions, inbr_subpops) # FST of admixed individuals Fst <- fst_admix(admix_proportions, inbr_subpops) # draw all random allele freqs and genotypes out <- draw_all_admix(admix_proportions, inbr_subpops, m_loci) # genotypes X <- out$X # ancestral allele frequencies (AFs) p_anc <- out$p_anc # OR... draw each vector or matrix separately # provided for additional flexibility # ancestral AFs p_anc <- draw_p_anc(m_loci) # independent subpops (intermediate) AFs p_subpops <- draw_p_subpops(p_anc, inbr_subpops) # individual-specific AFs p_ind <- make_p_ind_admix(p_subpops, admix_proportions) # genotypes X <- draw_genotypes_admix(p_ind)
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