crossover: Simulate crossover locations.

In DominikMueller64/Meiosis: Simulation of Meiosis in Plant Breeding Research

Description

Simulate crossover locations on a single meiotic product using the Stahl model.

Usage

crossover(L, m, p, obligate_chiasma, Lstar)

Arguments

L	Double. Length of the chromosome in cM.
m	Integer. The interference parameter (m = 0 is no interference).
p	Double. Proportion of chiasmata from no-interference mechanism. (p = 0 gives pure chi-square model)
obligate_chiasma	Logical. If TRUE, require an obligate chiasma on the 4-strand bundle at meiosis. Only possible if all chromosomes are longer than 50 cM.
Lstar	Double. Reduced chromosome length as produced by calc_Lstar.

Details

This function is an R-wrapper of an underlying C++ routine. It is not intended for direct usage, but exposed for completeness.

Value

Double Vector. Crossover locations.

Model

Chiasma locations are a superposition of two processes: a proportion p exhibiting no interference, and a proportion (1 - p) following the chi-square model with interference parameter m. Crossover locations are derived by thinning the chiasma locations with probability 1/2.

Simulations are under the Stahl model with the interference parameter being an integer. This is an extension of the chi-square model, but with chiasmata being the superposition of two processes, one following the chi-square model and the other exhibiting no interference.

References

Copenhaver, G. P., Housworth, E. A. and Stahl, F. W. (2002) Crossover interference in arabidopsis. Genetics 160, 1631–1639.

Foss, E., Lande, R., Stahl, F. W. and Steinberg, C. M. (1993) Chiasma interference as a function of genetic distance. Genetics 133, 681–691.

Zhao, H., Speed, T. P. and McPeek, M. S. (1995) Statistical analysis of crossover interference using the chi-square model. Genetics 139, 1045–1056.

Examples

Meiosis::crossover(300, 10, 0.5, FALSE, 300)

DominikMueller64/Meiosis documentation built on May 6, 2019, 2:52 p.m.