sim.ri: Simulate a recombinant inbred line

In kbroman/ricalc: Calculations for Recombinant Inbred Lines

Simulate a recombinant inbred line

Description

Simulates alleles for a multiple-strain RI line, using the chi-square model for interference at meiosis, performing inbreeding by selfing or sibling mating, until complete fixation has occurred.

Usage

sim.ri(L, sexsp=1, type=c("selfing","sibmating"),
       n.strains=c("2","4","8"),
       xchr=FALSE, m=10, obligate.chiasma=FALSE)

Arguments

L	Length of chromosome(s) in cM; either a vector or a single number.
sexsp	Female:male recombination rate (must be > 0)
type	Indicates whether the inbreeding is by selfing or by sibling mating.
n.strains	Number of initial parental strains.
xchr	If length(L)==1 and type="sibmating", this indicates to simulate the X chromosome. If length(L) > 1, the chromosomes named "X" or "x" are taken to be the X chromosome and all others are assumed to be autosomes.
m	The interference parameter (a non-negative integer). m=0 corresponds to no interference; m>0 corresponds to positive crossover interference.
obligate.chiasma	Indicates whether there is an obligate chiasma on the four-strand bundle.

Details

Meiosis is simulated by the chi-square model (see Zhao et al. 1995), with the possibility of requiring an obligate chiasma on the four-strand bundle at meiosis.

Inbreeding is performed until complete fixation. Of course, we assume no mutation and no selection.

Value

If length(L)==1, the output is a two-row matrix whose first row consists of the locations of exchanges along the recombinant inbred chromosome (0 and L are included). The second row contains the allele (coded 1, 2, ..., 8) in the interval to the left. Attributes "prop.het" and "num.het" are included which contain the proportion of the genome that is not yet fixed and the number of segments of such heterozygosity, respectively, after each generation of inbreeding. The attribute "nubreak" gives the number of unique breakpoints at each generation.

If length(L)>1, the output is a list of length length(L), with each component being a two-row matrix, as above. The overall list also has attributes "prop.het" and "num.het", specifying the proportion of the entire genome that has not yet been fixed and the number of segments of such heterozygosity, respectively, after each generation of inbreeding.

Author(s)

Karl W Broman, [e-mail]

References

Haldane, J. B. S. and Waddington, C. H. (1931) Inbreeding and linkage. Genetics 16, 357–374.

Broman, K. W. (2005) The genomes of recombinant inbred lines. Genetics 169, 1133–1146.

Broman, K. W., Rowe, L. B., Churchill, G. A. and Paigen, K. (2002) Crossover interference in the mouse. Genetics 160, 1123–1131.

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

See Also

sim.ri

Examples

data(mouseL)
ri <- sim.ri(mouseL, type="selfing", n.str="8")

kbroman/ricalc documentation built on May 17, 2023, 11:54 p.m.