est.map {qtl} | R Documentation |

## Estimate genetic maps

### Description

Uses the Lander-Green algorithm (i.e., the hidden Markov model
technology) to re-estimate the genetic map for an experimental cross.

### Usage

est.map(cross, error.prob=0,
map.function=c("haldane","kosambi","c-f","morgan"), maxit=4000,
tol=1e-4, sex.sp=TRUE, trace=FALSE)

### Arguments

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

`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. |

`maxit` |
Maximum number of EM iterations to perform. |

`tol` |
Tolerance for determining convergence. |

`sex.sp` |
Indicates whether to estimate sex-specific maps; this is
used only for the 4-way cross. |

`trace` |
Logical; indicates whether to print initial and final
estimates of the recombination fractions for each chromosome. |

### Value

A `map`

object; a list whose components (corresponding to
chromosomes) are either vectors of marker positions (in cM) or
matrices with two rows of sex-specific marker positions.
The maximized log likelihood for each chromosome is saved as an
attribute named `loglik`

.

### Author(s)

Karl W Broman, kbroman@jhsph.edu

### References

Lange, K. (1999) *Numerical analysis for statisticians*.
Springer-Verlag. Sec 23.3.

Rabiner, L. R. (1989) A tutorial on hidden Markov models and selected
applications in speech recognition. *Proceedings of the IEEE*
**77**, 257–286.

Lander, E. S. and Green, P. (1987) Construction of multilocus genetic linkage
maps in humans. *Proc. Natl. Acad. Sci. USA* **84**, 2363–2367.

### See Also

`plot.map`

, `replace.map`

,
`est.rf`

### Examples

data(fake.f2)
newmap <- est.map(fake.f2)
logliks <- sapply(newmap, attr, "loglik")
plot.map(fake.f2, newmap)
fake.f2 <- replace.map(fake.f2, newmap)

[Package

*qtl* version 0.98-57

Index]