sim.ri | R Documentation |
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.
sim.ri(L, sexsp=1, type=c("selfing","sibmating"),
n.strains=c("2","4","8"),
xchr=FALSE, m=10, obligate.chiasma=FALSE)
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 |
m |
The interference parameter (a non-negative integer).
|
obligate.chiasma |
Indicates whether there is an obligate chiasma on the four-strand bundle. |
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.
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.
Karl W Broman, broman@wisc.edu
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.
sim.ri
data(mouseL)
ri <- sim.ri(mouseL, type="selfing", n.str="8")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.