R: Simulate a QTL experiment

sim.cross {qtl}

R Documentation

Simulate a QTL experiment

Description

Simulates data for a QTL experiment using a model in which QTLs act additively. A backcross, intercross, or phase-known 4-way cross may be simulated.

Usage

sim.cross(map, model=NULL, n.ind=100, type=c("f2", "bc", "4way"),
          error.prob=0, missing.prob=0, partial.missing.prob=0,
          keep.qtlgeno=FALSE,error.ind=TRUE,
          map.function=c("haldane","kosambi","c-f"))

Arguments

`map`	A list of length n.chr; its components are vectors containing the marker locations on each of the chromosomes.
`model`	A matrix where each row corresponds to a different QTL, and gives the chromosome number, cM position and effects of the QTL.
`n.ind`	Number of individuals to simulate.
`type`	Indicates whether to simulate an intercross ("f2"), a backcross ("bc"), or a 4-way cross ("4way").
`error.prob`	The genotyping error rate to simulate.
`missing.prob`	The rate of missing genotypes to simulate.
`partial.missing.prob`	When simulating an intercross or 4-way cross, this gives the rate at which markers will be incompletely informative (i.e., dominant or recessive).
`keep.qtlgeno`	If TRUE, genotypes for the simulated QTLs are not removed from the marker genotype data or genetic maps.
`error.ind`	If TRUE, and if `error.prob > 0`, the components of `geno` will each contain a matrix, `errors`, with 1's indicating a simulated genotyping error.
`map.function`	Indicates whether to use the Haldane, Kosambi or Carter-Falconer map function when converting genetic distances into recombination fractions.

Details

Meiosis is assumed to exhibit no crossover interference. If one of the chromosomes has class X, it is assumed to be the X chromosome, and is assumed to be segregating in the cross. Thus, in an intercross, it is segregating like a backcross chromosome. In a 4-way cross, a second phenotype, sex, will be generated. In order to ensure that the code is relatively easy to read, simulation is actually performed in a set of subfunctions, sim.cross.bc, sim.cross.f2, and sim.cross.4way.

Value

An object of class cross. See read.cross for details.

Author(s)

Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

Examples

map <- sim.map()
fake <- sim.cross(map,type="f2", model = rbind(c(1,20,1,2),c(5,20,0.5,0.5)))

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