R: Simulate genotypes given observed marker data

sim.geno {qtl} | R Documentation

## Simulate genotypes given observed marker data

### Description

Uses the hidden Markov model technology to simulate from the joint distribution Pr(g | O) where g is the underlying genotype vector and O is the observed multipoint marker data, with possible allowance for genotyping errors.

### Usage

    sim.geno(cross, n.draws=16, step=0, off.end=0, error.prob=0.0001,
             map.function=c("haldane","kosambi","c-f","morgan"),
             stepwidth=c("fixed", "variable", "max"))

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`n.draws` | Number of simulation replicates to perform.
`step` | Maximum distance (in cM) between positions at which the simulated genotypes will be drawn, though for `step=0`, genotypes are drawn only at the marker locations.
`off.end` | Distance (in cM) past the terminal markers on each chromosome to which the genotype simulations will be carried.
`error.prob` | Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).
`map.function` | Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions.
`stepwidth` | Indicates whether the intermediate points should with fixed or variable step sizes. We recommend using `"fixed"`; `"variable"` is included for the qtlbim package (http://www.ssg.uab.edu/qtlbim). The `"max"` option inserts the minimal number of intermediate points so that the maximum distance between points is `step`.

### Details

After performing the forward-backward equations, we draw from Pr(g[1] = v | O) and then Pr(g[k+1] = v | O, g[k] = u).

In the case of the 4-way cross, with a sex-specific map, we assume a constant ratio of female:male recombination rates within the inter-marker intervals.

### Value

The input `cross` object is returned with a component, `draws`, added to each component of `cross$geno`. This is an array of size [n.ind x n.pos x n.draws] where n.pos is the number of positions at which the simulations were performed and n.draws is the number of replicates. Attributes `"error.prob"`, `"step"`, and `"off.end"` are set to the values of the corresponding arguments, for later reference.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`calc.genoprob`, `argmax.geno`

### Examples

    data(fake.f2)

    fake.f2 <- sim.geno(fake.f2, step=2, n.draws=8)

[Package qtl version 1.41-6 Index]