R: Estimate pairwise recombination fractions

est.rf {qtl} | R Documentation

## Estimate pairwise recombination fractions

### Description

Estimate the sex-averaged recombination fraction between all pairs of genetic markers.

### Usage

    est.rf(cross, maxit=10000, tol=1e-6)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`maxit` | Maximum number of iterations for the EM algorithm (not used with backcrosses).
`tol` | Tolerance for determining convergence (not used with backcrosses).

### Details

For a backcross, one can simply count recombination events. For an intercross or 4-way cross, a version of the EM algorithm must be used to estimate recombination fractions. (Since, for example, in an intercross individual that is heterozygous at two loci, it is not known whether there were 0 or 2 recombination events.) Note that, for the 4-way cross, we estimate sex-averaged recombination fractions.

### Value

The input `cross` object is returned with a component, `rf`, added. This is a matrix of size (tot.mar x tot.mar). The diagonal contains the number of typed meioses per marker, the lower triangle contains the estimated recombination fractions, and the upper triangle contains the LOD scores (testing rf = 0.5).

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`plotRF`, `pull.rf`, `plot.rfmatrix`, `est.map`, `badorder`, `checkAlleles`

### Examples

    data(badorder)
    badorder <- est.rf(badorder)
    plotRF(badorder)

[Package qtl version 1.46-2 Index]