umx (version 4.0.0)

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<U+2013>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

See Also

Other Teaching and testing Functions: tmx_is.identified(), umx

Examples

# NOT RUN {
library(umx);

# }
# NOT RUN {
# =========================
# = 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)
# }
# NOT RUN {
# }