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bnpsd

Simulate Genotypes from the BN-PSD Admixture Model

The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Functions (13)

admix_prop_1d_circular

Construct admixture proportion matrix for circular 1D geography

admix_prop_1d_linear

Construct admixture proportion matrix for 1D geography

admix_prop_indep_subpops

Construct admixture proportion matrix for independent subpopulations

bnpsd

A package for modeling and simulating an admixed population

coanc_admix

Construct the coancestry matrix of an admixture model

coanc_to_kinship

Transform coancestry matrix to kinship matrix

draw_all_admix

Simulate random allele frequencies and genotypes from the BN-PSD admixture model

draw_genotypes_admix

Draw genotypes from the admixture model

draw_p_anc

Draw random Uniform or Beta ancestral allele frequencies

draw_p_subpops

Draw allele frequencies for independent subpopulations

fixed_loci

Identify fixed loci

fst_admix

Calculate FST for the admixed individuals

make_p_ind_admix

Construct individual-specific allele frequency matrix under the PSD admixture model

bnpsd

Simulate Genotypes from the BN-PSD Admixture Model

v1.2.3
GPL-3
Authors
Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>), John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Initial release

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