Description Usage Arguments Details Value Model References Examples
Simulate crossover locations on a single meiotic product using the Stahl model.
1 | crossover(L, m, p, obligate_chiasma, Lstar)
|
L |
Double. Length of the chromosome in cM. |
m |
Integer. The interference parameter ( |
p |
Double. Proportion of chiasmata from no-interference mechanism.
( |
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 |
This function is an R-wrapper of an underlying C++ routine. It is not intended for direct usage, but exposed for completeness.
Double Vector. Crossover locations.
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.
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.
1 |
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