sim.ped | R Documentation |
Simulates alleles for a general pedigree, using the chi-square model for interference at meiosis.
sim.ped(pedigree, L, sexsp=1, xchr=FALSE, m=10, obligate.chiasma=FALSE)
pedigree |
A matrix with rows corresponding to individuals and
columns being individual identifiers ( |
L |
Length of chromosome in cM. |
sexsp |
Female:male recombination rate (must be > 0) |
xchr |
If TRUE, simulate the X chromosome. |
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.
The pedigree
matrix must have columns named "id"
,
"sex"
, "mom"
/"dam"
and
"dad"
/"sire"
. Other columns are ignored.
Founders should have 0 in the mom and dad columns; others should have
the identifiers for the mom and dad. Each individual must have either
both parents in the matrix or neither.
The output is a list with length equal to the number of rows in
pedigree
. Each component is itself a list with two components,
the maternal and paternal chromosomes. These are matrices with two
rows: The first row consists of the locations of exchanges
(0 and L
are included); the second row
contains the allele (coded 1, 2, ..., no. founders) in the interval to the
left.
Karl W Broman, broman@wisc.edu
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
, genAILped
, convert2gen
ailped <- genAILped(ngen=5, npairs=5, sibship.size=2)
aildat <- sim.ped(ailped, 100)
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