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=4000, tol=1e-4)

### 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 it shows 0 or 2 recombinations.) 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, kbroman@jhsph.edu

### See Also

`plot.rf`

, `est.map`

,
`badorder`

### Examples

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

[Package

*qtl* version 0.98-57

Index]