tmx_genotypic_effect | R Documentation |

`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

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

`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) |

optional plot

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

Other Teaching and testing Functions:
`tmx_is.identified()`

,
`umx`

```
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 = p + ggplot2::geom_point()
# p + ggplot2::geom_text(hjust = 0, nudge_x = 0.05, label= "x")
# ggsave(paste0(base, "c03_genotypic_effect_by_gene_dose.pdf"), width = 4.6, height = 4.6)
```

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