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bnpsd (version 1.0.4)

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

364

Version

1.0.4

License

GPL-3

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Maintainer

Alejandro Ochoa

Last Published

February 12th, 2019

Functions in bnpsd (1.0.4)

rpanc

Draw uniform ancestral allele frequencies
q1d

Construct admixture proportion matrix for 1D geography
rpint

Draw intermediate subpopulation allele frequencies
rpiaf

Construct individual-specific allele frequency matrix
fst

Calculate FST for the admixed individuals
coanc

Construct the coancestry matrix of an admixture model
q1dc

Construct admixture proportion matrix for circular 1D geography
qis

Construct admixture proportion matrix for independent subpopulations
bnpsd

A package for modeling and simulating an admixed population
rbnpsd

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

Draw genotypes from the admixture model
coanc_to_kinship

Transform coancestry matrix to kinship matrix
fixed_loci

Identify fixed loci