| ripple {qtl} | R Documentation |
Investigate different marker orders for a given chromosome, comparing all possible permutations of a sliding window of markers.
ripple(cross, chr, window=4, error.prob=0,
map.function=c("haldane","kosambi","c-f"),
maxit=1000, tol=1e-5, sex.sp=TRUE)
cross |
An object of class cross. See
read.cross for details. |
chr |
The chromosome to investigate. Only one chromosome is allowed. |
window |
Number of markers to include in the sliding window of permuted markers. Larger numbers result in the comparison of a greater number of marker orders, but will require a considerable increase in computation time. |
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. |
Calculations are done by first constructing a matrix of marker orders
and then making repeated calls to the R function
est.map. Of course, it would be faster to do
everything within C, but this was a lot easier to code.
A matrix, given class "ripple"; the first set of columns are marker indices describing the order. The last two columns are lod (log base 10 likelihood ratios) comparing each order to the initial order and the estimated chromosome length for the given order.
Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html
summary.ripple, est.map,
est.rf
data(fake.f2) output <- ripple(fake.f2,7,2) summary(output,2)