est.rf {qtl}R Documentation

Estimate pairwise recombination fractions

Description

Estimate the sex-averaged recombination fraction between all pairs of typed markers.

Usage

est.rf(cross, maxit=1000, tol=1e-6)

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 cross object in the input 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
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

See Also

plot.rf, est.map

Examples

data(fake.f2)
fake.f2 <- est.rf(fake.f2)
plot.rf(fake.f2)
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