bnpsd: draw_p_subpops – R documentation

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draw_p_subpops

Draw allele frequencies for independent subpopulations

Description

The allele frequency matrix P for m_loci loci (rows) and k_subpops independent subpopulations (columns) are drawn from the Balding-Nichols distribution with ancestral allele frequencies p_anc and FST parameters inbr_subpops equivalent to P[ i, j ] <- rbeta( 1, nu_j * p_anc[i], nu_j * ( 1 - p_anc[i] ) ), where nu_j <- 1 / inbr_subpops[j] - 1. The actual function is more efficient than the above code.

Usage

draw_p_subpops(p_anc, inbr_subpops, m_loci = NA, k_subpops = NA)

Arguments

`p_anc`	The scalar or length-`m_loci` vector of ancestral allele frequencies per locus.
`inbr_subpops`	The length-`k_subpops` vector of subpopulation FST values.
`m_loci`	If `p_anc` is scalar, optionally provide the desired number of loci (lest only one locus be simulated). Stops if both `length(p_anc) > 1` and `m_loci` is not `NA` and they disagree.
`k_subpops`	If `inbr_subpops` is a scalar, optionally provide the desired number of subpopulations (lest a single subpopulation be simulated). Stops if both `length(inbr_subpops) > 1` and `k_subpops` is not `NA` and they disagree.

Value

The m_loci-by-k_subpops matrix of independent subpopulation allele frequencies

Examples

# a typical, non-trivial example
# number of loci
m_loci <- 10
# random vector of ancestral allele frequencies
p_anc <- draw_p_anc(m_loci)
# FST values for two subpops
inbr_subpops <- c(0.1, 0.3)
# matrix of intermediate subpop allele freqs
p_subpops <- draw_p_subpops(p_anc, inbr_subpops)

# special case of scalar p_anc
p_subpops <- draw_p_subpops(p_anc = 0.5, inbr_subpops, m_loci = m_loci)
stopifnot ( nrow( p_subpops ) == m_loci )

# special case of scalar inbr_subpops
k_subpops <- 2
p_subpops <- draw_p_subpops(p_anc, inbr_subpops = 0.2, k_subpops = k_subpops)
stopifnot ( ncol( p_subpops ) == k_subpops )

# both main parameters scalars but return value still matrix
p_subpops <- draw_p_subpops(p_anc = 0.5, inbr_subpops = 0.2, m_loci = m_loci, k_subpops = k_subpops)
stopifnot ( nrow( p_subpops ) == m_loci )
stopifnot ( ncol( p_subpops ) == k_subpops )

# passing scalar parameters without setting dimensions separately results in a 1x1 matrix
p_subpops <- draw_p_subpops(p_anc = 0.5, inbr_subpops = 0.2)
stopifnot ( nrow( p_subpops ) == 1 )
stopifnot ( ncol( p_subpops ) == 1 )

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