Estimate pairwise recombination fractions
Estimate the sex-averaged recombination fraction between all pairs of genetic markers.
est.rf(cross, maxit=10000, tol=1e-6)
cross |
An object of class |
maxit |
Maximum number of iterations for the EM algorithm (not used with backcrosses). |
tol |
Tolerance for determining convergence (not used with backcrosses). |
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 there were 0 or 2 recombination events.) Note that, for the 4-way cross, we estimate sex-averaged recombination fractions.
The input cross object 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).
Karl W Broman, broman@wisc.edu
data(badorder) badorder <- est.rf(badorder) plotRF(badorder)
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