create_xoparam: Create a parameter list for simulating crossovers.

In Meiosis: Simulation of Meiosis in Plant Breeding Research

Description

Create a parameter list for simulating crossover locations on a single meiotic product using the Stahl model.

Usage

create_xoparam(L, m = 0L, p = 1, obligate_chiasma = FALSE)

Arguments

L	Double vector. Chromosome lengths in CentiMorgan (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.

Details

If obligate_chiasma = TRUE and all chromsome are longer than 50 cM, reduced chromosome length with be internally calculated (calc_Lstar) that will give the target expected number of chiasmata when conditioning on there being at least one chiasma on the four-strand bundle.

This description is adopted from the simcross package.

Value

A nested list as long as the number of chromosomes with parameters used for simulating crossover events.

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

create_xoparam(L = c(50.5, 100.1, 133.5))

Meiosis documentation built on May 29, 2017, 3:46 p.m.