qtl (version 0.92-3)

est.map: 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"), 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 or Carter-Falconer 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.

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)