gamfreq: Gamete frequencies under a generalized model
In segtest: Tests for Segregation Distortion in Polyploids
gamfreq R Documentation
Gamete frequencies under a generalized model
Description
Returns the gamete frequencies for autopolyploids, allopolyploids,
and segmental allopolyploids, accounting for the effects of double
reduction and partial preferential pairing.
Usage
gamfreq(
g,
ploidy,
gamma = NULL,
alpha = NULL,
beta = NULL,
type = c("mix", "polysomic"),
add_dr = TRUE
)
Arguments
g
Parent genotype.
ploidy
Parent ploidy. Should be even, and between 2 and 20 (inclusive).
Let me know if you need the ploidy to be higher. I can update
the package really easily.
gamma
The mixture proportions for the pairing configurations.
The proportions are in the same order the configurations in
seg. See Gerard et al (2018) for details on
pairing configurations.
alpha
The double reduction rate(s) (if using). Defaults to 0's.
beta
The double reduction adjustment for simplex markers if
type = "mix" and add_dr = TRUE. Assumed to be 0 by default.
type
Either "mix", meaning a mixture model of
pairing configurations, or "polysomic" for polysomic inheritance.
add_dr
A logical. If type = "polysomic", then the double
double reduction rate ("alpha") will be used no matter the
value of add_dr, so set alpha = 0 if you don't want it.
But if type = "mix" then we will incorporate double reduction
only in simplex markers (where it matters the most, and where
preferential pairing does not operate).
Value
The vector of gamete frequencies. Element i is the
probability a gamete has genotype i - 1.
Models
If type = "polysomic", then the gamete frequencies correspond
to those of Huang et al (2019). Those formulas are for general multiallelic
loci, so see also Appendix G of Gerard (2022) for special case of
biallelic loci. The relevant parameter is alpha, a vector of
length floor(ploidy / 4), where alpha[[i]] is the
probability that there are i pairs of double reduced alleles
in a gamete. The theoretical upper bound on alpha is given in
drbounds().
If type = "mix" and add_dr = FALSE, then the gamete
frequencies correspond to the pairing configuration model of
Gerard et al (2018). This model states that the gamete frequencies are
a convex combination of the disomic inheritance frequencies. The weights
of this convex combination are provided in the gamma parameter. The
total number of disomic segregation patterns is given by
n_pp_mix(). The order of these segregation patterns used is
the order in seg.
The model for type = "mix" and add_dr = TRUE is the same
as for type = "mix" and add_dr = FALSE except at
parental simplex loci. At such loci, there are no effects of preferential
pairing, and so the option add_dr = TRUE allows for the effects
of double reduction at simplex loci. The relevant parameter here is
beta. The first three gamete frequencies at simplex loci are
c(0.5 + beta, 0.5 - 2 * beta, beta), and the rest are 0. The
upper bound on beta for two different models are given by
beta_bounds().
Author(s)
David Gerard
References
Gerard, D. (2023). Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics, 79(3), 2143-2156. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/biom.13722")}
Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping polyploids from messy sequencing data. Genetics, 210(3), 789-807. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301468")}
Huang, K., Wang, T., Dunn, D. W., Zhang, P., Cao, X., Liu, R., & Li, B. (2019). Genotypic frequencies at equilibrium for polysomic inheritance under double-reduction. G3: Genes, Genomes, Genetics, 9(5), 1693-1706. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.119.400132")}
Examples
## Various duplex models
gamfreq(g = 2, ploidy = 4, gamma = c(0, 1), type = "mix")
gamfreq(g = 2, ploidy = 4, gamma = c(1, 0), type = "mix")
gamfreq(g = 2, ploidy = 4, gamma = c(0.5, 0.5), type = "mix")
gamfreq(g = 2, ploidy = 4, alpha = 0, type = "polysomic")
gamfreq(g = 2, ploidy = 4, alpha = 1/6, type = "polysomic")
## Various simplex models
gamfreq(g = 1, ploidy = 4, beta = 1/24, gamma = 1, type = "mix", add_dr = TRUE)
gamfreq(g = 1, ploidy = 4, alpha = 1/6, type = "polysomic")
gamfreq(g = 1, ploidy = 4, gamma = 1, type = "mix", add_dr = FALSE)
gamfreq(g = 1, ploidy = 4, alpha = 0, type = "polysomic")
segtest documentation built on July 1, 2025, 1:07 a.m.
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| gamfreq | R Documentation |
Gamete frequencies under a generalized model
Description
Returns the gamete frequencies for autopolyploids, allopolyploids, and segmental allopolyploids, accounting for the effects of double reduction and partial preferential pairing.
Usage
gamfreq(
g,
ploidy,
gamma = NULL,
alpha = NULL,
beta = NULL,
type = c("mix", "polysomic"),
add_dr = TRUE
)
Arguments
g |
Parent genotype. |
ploidy |
Parent ploidy. Should be even, and between 2 and 20 (inclusive). Let me know if you need the ploidy to be higher. I can update the package really easily. |
gamma |
The mixture proportions for the pairing configurations.
The proportions are in the same order the configurations in
|
alpha |
The double reduction rate(s) (if using). Defaults to 0's. |
beta |
The double reduction adjustment for simplex markers if
|
type |
Either |
add_dr |
A logical. If |
Value
The vector of gamete frequencies. Element i is the
probability a gamete has genotype i - 1.
Models
If type = "polysomic", then the gamete frequencies correspond
to those of Huang et al (2019). Those formulas are for general multiallelic
loci, so see also Appendix G of Gerard (2022) for special case of
biallelic loci. The relevant parameter is alpha, a vector of
length floor(ploidy / 4), where alpha[[i]] is the
probability that there are i pairs of double reduced alleles
in a gamete. The theoretical upper bound on alpha is given in
drbounds().
If type = "mix" and add_dr = FALSE, then the gamete
frequencies correspond to the pairing configuration model of
Gerard et al (2018). This model states that the gamete frequencies are
a convex combination of the disomic inheritance frequencies. The weights
of this convex combination are provided in the gamma parameter. The
total number of disomic segregation patterns is given by
n_pp_mix(). The order of these segregation patterns used is
the order in seg.
The model for type = "mix" and add_dr = TRUE is the same
as for type = "mix" and add_dr = FALSE except at
parental simplex loci. At such loci, there are no effects of preferential
pairing, and so the option add_dr = TRUE allows for the effects
of double reduction at simplex loci. The relevant parameter here is
beta. The first three gamete frequencies at simplex loci are
c(0.5 + beta, 0.5 - 2 * beta, beta), and the rest are 0. The
upper bound on beta for two different models are given by
beta_bounds().
Author(s)
David Gerard
References
Gerard, D. (2023). Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics, 79(3), 2143-2156. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/biom.13722")}
Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping polyploids from messy sequencing data. Genetics, 210(3), 789-807. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301468")}
Huang, K., Wang, T., Dunn, D. W., Zhang, P., Cao, X., Liu, R., & Li, B. (2019). Genotypic frequencies at equilibrium for polysomic inheritance under double-reduction. G3: Genes, Genomes, Genetics, 9(5), 1693-1706. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.119.400132")}
Examples
## Various duplex models
gamfreq(g = 2, ploidy = 4, gamma = c(0, 1), type = "mix")
gamfreq(g = 2, ploidy = 4, gamma = c(1, 0), type = "mix")
gamfreq(g = 2, ploidy = 4, gamma = c(0.5, 0.5), type = "mix")
gamfreq(g = 2, ploidy = 4, alpha = 0, type = "polysomic")
gamfreq(g = 2, ploidy = 4, alpha = 1/6, type = "polysomic")
## Various simplex models
gamfreq(g = 1, ploidy = 4, beta = 1/24, gamma = 1, type = "mix", add_dr = TRUE)
gamfreq(g = 1, ploidy = 4, alpha = 1/6, type = "polysomic")
gamfreq(g = 1, ploidy = 4, gamma = 1, type = "mix", add_dr = FALSE)
gamfreq(g = 1, ploidy = 4, alpha = 0, type = "polysomic")
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