umx: tmx_genotypic_effect – R documentation

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tmx_genotypic_effect

Graphical display of genotypic effects.

Description

tmx_genotypic_effect allows you to explore the concept of genotypic effect at a locus. With it, you can interactively explore the effects of allele frequency, additive variance, and dominance.

This function lets you explore the simplest two–allele system (B and b), with three possible genotypes, BB, Bb, and bb.

The point between the two homozygotes is m – the mean effect of the homozygous genotypes.

Parameter a is half the measured phenotypic difference between the homozygotes BB and bb. It corresponds to the additive effect of each additional B allele, relative to the bb phenotype.

Parameter d is the deviation of the heterozygote Bb phenotype from the homozygote mid-point m. It corresponds to the non-additive (dominance) effect of the B allele. The heterozygote phenotype may lie on either side of m and the sign of d will vary accordingly.

Old system from book ed 2:

Adapted from Mather and Jinks, 1977, p. 32). See book issue old-style nomenclature https://github.com/tbates/BGBook/issues/23

u = Frequency of the dominant allele (now = p). v = Frequency of the recessive allele (now = q).

m = midpoint between the two homozygotes d = half the difference between the two homozygote (now a)

h = deviation of the heterozygote from m (now = d)

New system:

u and v -> p and q

d and h -> a and d

See BGBook issue 23

Usage

tmx_genotypic_effect(p = 0.75, q = (1 - p), a = 0.5, d = 0, m = 0, show = TRUE)

Arguments

`p`	The frequency of the B allele (Default .5)
`q`	The frequency of the b allele (Default 1-p)
`a`	Half the difference between the two homozygote phenotypes (Default .5)
`d`	The deviation of the heterozygote from m (Default 0)
`m`	The value of the midpoint between the homozygotes (Default 0)
`show`	Whether to draw the plot or just return it (Default = TRUE)

Value

optional plot

References

Neale, M. C. (2005). Quantitative Genetics. In Encyclopedia of Life Sciences. New York: John Wiley & Sons, Ltd. pdf

Examples

library(umx);


# =========================
# = Pure additivity: d= 0 =
# =========================
tmx_genotypic_effect(p = .5, a = 1, d = 0, m = 0, show = TRUE);

# =============================
# = Complete dominance: a=d=1 =
# =============================
tmx_genotypic_effect(p = .5, q =.5, a = 1, d = 1, m = 0, show = TRUE);

# ===========================
# = Over dominance: a< d =1 =
# ===========================
tmx_genotypic_effect(p = .5, q =.5, a =.5, d = 1, m = 0)

p = tmx_genotypic_effect(p = .5, q = .5, a = 1, d = .5, m = 0, show = TRUE); 
# p + ggplot2::geom_point() + ggplot2::geom_text(hjust = 0, nudge_x = 0.05)
# ggsave(paste0(base, "c03_genotypic_effect_by_gene_dose.pdf"), width = 4.6, height = 4.6)

umx

Structural Equation Modeling and Twin Modeling in R

v4.10.10

GPL-3

Authors

Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>), Gillespie Nathan [wit], Michael Zakharin [wit], Brenton Wiernik [ctb], Joshua N. Pritikin [ctb], Michael C. Neale [ctb], Hermine Maes [ctb]

Initial release

2021-11-30