Meiosis (version 1.0.2)

create_xoparam: Create a parameter list for simulating crossovers.

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.

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.

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 https://github.com/kbroman/simcross package.

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))