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]