bnpsd: A package for modeling and simulating an admixed population

In bnpsd: Simulate Genotypes from the BN-PSD Admixture Model

Description

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).

Author(s)

Maintainer: Alejandro Ochoa [e-mail] (ORCID)

Authors:

• John D. Storey [e-mail] (ORCID)

See Also

Useful links:

• https://github.com/StoreyLab/bnpsd/

• Report bugs at https://github.com/StoreyLab/bnpsd/issues

Examples

# 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 )

### Examples with a tree for intermediate subpopulations

# tree allows for correlated subpopulations
# (prev examples had independent subpopulations)

# best to start by specifying tree in Newick string format
tree_str <- '(S1:0.1,(S2:0.1,S3:0.1)N1:0.1)T;'
# and turn it into `phylo` object using the `ape` package
library(ape)
tree_subpops <- read.tree( text = tree_str )
# true coancestry matrix corresponding to this tree
coanc_subpops <- coanc_tree( tree_subpops )

# admixture proportions from 1D geography
# (constructed again but for k=3 tree)
k_subpops <- nrow( coanc_subpops )
admix_proportions <- admix_prop_1d_linear( n_ind, k_subpops, sigma = 0.5 )

# get pop structure parameters of the admixed individuals
# the coancestry matrix
coancestry <- coanc_admix( admix_proportions, coanc_subpops )
# FST of admixed individuals
Fst <- fst_admix( admix_proportions, coanc_subpops )

# draw all random allele freqs and genotypes, tree version
out <- draw_all_admix( admix_proportions, tree_subpops = tree_subpops, m_loci = m_loci )
# genotypes
X <- out$X
# ancestral allele frequencies (AFs)
p_anc <- out$p_anc

# OR... draw tree subpops (intermediate) AFs separately
p_subpops_tree <- draw_p_subpops_tree( p_anc, tree_subpops )

bnpsd documentation built on Aug. 25, 2021, 5:07 p.m.