ripple {qtl}R Documentation

Compare marker orders

Description

Investigate different marker orders for a given chromosome, comparing all possible permutations of a sliding window of markers.

Usage

ripple(cross, chr, window=4, method=c("countxo","likelihood"),
       error.prob=0, map.function=c("haldane","kosambi","c-f","morgan"),
       maxit=4000, tol=1e-4, sex.sp=TRUE)

Arguments

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.
method Indicates whether to compare orders by counting the number of obligate crossovers, or by a likelihood analysis.
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, Carter-Falconer, or Morgan 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.

Details

For method="likelihood", 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.

For method="countxt", calculations are done within C.

Value

A matrix, given class "ripple"; the first set of columns are marker indices describing the order. In the case of method="countxo", the last column is the number of obligate crossovers for each particular order. In the case of method="likelihood", the last two columns are LOD scores (log base 10 likelihood ratios) comparing each order to the initial order and the estimated chromosome length for the given order. Positive LOD scores indicate that the alternate order has more support than the original.

Author(s)

Karl W Broman, kbroman@jhsph.edu

See Also

summary.ripple, switch.order, est.map, est.rf

Examples

data(badorder)
rip7c <- ripple(badorder, chr=1, window=3)
summary(rip7c)

## Not run: 
rip2l <- ripple(badorder, chr=1, window=2, method="likelihood")
summary(rip2l)
## End(Not run)

badorder <- switch.order(badorder, 1, rip7c[2,])

[Package qtl version 0.98-57 Index]