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bnpsd (version 1.1.1)

Simulate Genotypes from the BN-PSD Admixture Model

Description

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 (2016) .

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install.packages('bnpsd')

Monthly Downloads

362

Version

1.1.1

License

GPL-3

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Last Published

May 15th, 2019

Functions in bnpsd (1.1.1)

admix_prop_1d_linear

Construct admixture proportion matrix for 1D geography
coanc-deprecated

Construct the coancestry matrix of an admixture model
draw_all_admix

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

Draw genotypes from the admixture model
rpanc-deprecated

Draw uniform ancestral allele frequencies
rbnpsd-deprecated

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

Draw genotypes from the admixture model
rpiaf-deprecated

Construct individual-specific allele frequency matrix under the PSD admixture model
q1dc-deprecated

Construct admixture proportion matrix for 1D geography
qis-deprecated

Construct admixture proportion matrix for independent subpopulations
draw_p_subpops

Draw allele frequencies for independent subpopulations
rpint-deprecated

Draw intermediate subpopulation allele frequencies
coanc_admix

Construct the coancestry matrix of an admixture model
coanc_to_kinship

Transform coancestry matrix to kinship matrix
make_p_ind_admix

Construct individual-specific allele frequency matrix under the PSD admixture model
q1d-deprecated

Construct admixture proportion matrix for 1D geography
bnpsd

A package for modeling and simulating an admixed population
admix_prop_1d_circular

Construct admixture proportion matrix for circular 1D geography
admix_prop_indep_subpops

Construct admixture proportion matrix for independent subpopulations
draw_p_anc

Draw random uniform ancestral allele frequencies
q1dc

Deprecated functions in package bnpsd.
fixed_loci

Identify fixed loci
fst_admix

Calculate FST for the admixed individuals