sim.ped: Simulate a general pedigree

In kbroman/ricalc: Calculations for Recombinant Inbred Lines

Simulate a general pedigree

Description

Simulates alleles for a general pedigree, using the chi-square model for interference at meiosis.

Usage

sim.ped(pedigree, L, sexsp=1, xchr=FALSE, m=10, obligate.chiasma=FALSE)

Arguments

pedigree	A matrix with rows corresponding to individuals and columns being individual identifiers ("id"), sex (0/1 or F/M), mom, and dad. Parents must precede their offspring.
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). 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.

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.

Value

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.

Author(s)

Karl W Broman, [e-mail]

References

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, genAILped, convert2gen

Examples

ailped <- genAILped(ngen=5, npairs=5, sibship.size=2)
aildat <- sim.ped(ailped, 100)

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