simStahl: Simulate crossover locations under the Stahl model

In xoi: Tools for Analyzing Crossover Interference

Simulate crossover locations under the Stahl model

Description

Simulate crossover locations under the Stahl model.

Usage

simStahl(
  n.sim,
  nu = 1,
  p = 0,
  L = 100,
  obligate_chiasma = FALSE,
  n.bins4start = 10000
)

Arguments

n.sim	Number of meiotic products to simulate.
nu	The interference parameter in the gamma model.
p	The proportion of chiasmata coming from the no-interference mechanism.
L	Chromosome length (in cM).
obligate_chiasma	Require an obligate chiasma (requires nu to be an integer; if nu is not an integer, it is rounded.
n.bins4start	We approximate the distribution of the location of the first crossover from the mechanism exhibiting interference using a even grid with this many bins. (Only if nu is not an integer.)

Details

The Stahl model is an extension to the gamma model, in which chiasmata occur according to two independent mechanisms. A proportion p come from a mechanism exhibiting no interference, and a proportion 1-p come from a mechanism in which chiasma locations follow a gamma model with interference parameter \nu.

Value

A vector of length n.sim, each element being empty (for products with no crossovers) or a vector of crossover locations, in cM. An attribute, L, contains the chromosome length in cM.

Author(s)

Karl W Broman, [e-mail]

References

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

Housworth, E. A. and Stahl, F. W. (2003) Crossover interference in humans. Am J Hum Genet 73, 188–197.

See Also

fitGamma(), qtl::sim.cross()

Examples

# simulations with no interference, chromosome of length 80 cM
xoNI <- simStahl(100, nu=1, p=0, L=80)

# simulations under gamma model with nu=7.6
xogamma <- simStahl(100, nu=7.6, p=0, L=80)

# simulations under Stahl model with nu=7.6, p=0.1
xostahl <- simStahl(100, nu=7.6, p=0.1, L=80)

# simulations under chi-square model with nu=11 (m=10) and obligate chiasma
xo_oblchi <- simStahl(100, nu=11, p=0, L=80, obligate_chiasma=TRUE)

# simulations under Stahl model with nu=11, p=0.1, and obligate chiasma
xo_oblchi_stahl <- simStahl(100, nu=11, p=0.1, L=80, obligate_chiasma=TRUE)

xoi documentation built on March 31, 2023, 9:27 p.m.