qtl (version 0.92-3)

ripple: 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, error.prob=0,
       map.function=c("haldane","kosambi","c-f"),
       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.

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.

Value

• A matrix, given class "ripple"; the first set of columns are marker indices describing the order. 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.

Details

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.

See Also

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

Examples

data(badorder)
rip2 <- ripple(badorder, 1, 2)
summary(rip2)

badorder <- switch.order(badorder, 1, rip2[2,])
rip2p <- ripple(badorder, 1, 2)
summary(rip2p)