bnpsd ("Balding-Nichols Pritchard-Stephens-Donnelly") R package is for simulating admixed populations.
bnpsd facilitates construction of admixed population structures and simulation of allele frequencies and genotypes from the BN-PSD admixture model.
This model combines the Balding-Nichols (BN) allele frequency model for the intermediate subpopulations with the Pritchard-Stephens-Donnelly (PSD) model of individual-specific admixture proportions.
This model enables the simulation of complex population structures, ideal for illustrating challenges in kinship coefficient and FST estimation.
Note that simulated loci are drawn independently (in linkage equilibrium).
The stable version of the package is now on CRAN and can be installed using
The current development version can be installed from the GitHub repository using
install.packages("devtools") # if needed library(devtools) install_github('StoreyLab/bnpsd', build_opts = c())
You can see the package vignette, which has more detailed documentation, by typing this into your R session:
This is a quick overview of the main
Define the population structure (in this case for 1D admixture scenario).
library(bnpsd) # 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_proportions, inbr_subpops)
Draw random allele frequencies and genotypes from this population structure.
# 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)
Ochoa, Alejandro, and John D. Storey. 2016a. "FST And Kinship for Arbitrary Population Structures I: Generalized Definitions." bioRxiv doi:10.1101/083915.
Ochoa, Alejandro, and John D. Storey. 2016b. "FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators." bioRxiv doi:10.1101/083923.