qtl (version 0.85-4)

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=1000, tol=1e-5, sex.sp=TRUE, print.rf=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.

print.rf

Indicates whether to print initial and final estimates of the recombination fractions for each chromosome. [This is mostly for debugging purposes.]

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.

Details

Calculations are done within the C function est_map. The maximized log likelihood for each chromosome is saved as an attribute named loglik.

References

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

LR Rabiner (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:257-286.

ES Lander, P Green (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363-2367.

See Also

plot.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)