switch.order {qtl}R Documentation

Switch the order of markers on a chromosome

Description

Switch the order of markers on a specified chromosome to a specified new order.

Usage

switch.order(cross, chr, order, error.prob=0,
                    map.function=c("haldane","kosambi","c-f","morgan"))

Arguments

cross An object of class cross. See read.cross for details.
chr The chromosome for which the marker order is to be switched.
order A vector of numeric indices defining the new marker order. The vector may have length two more than the number of markers, for easy in use with the output of the function ripple.
error.prob Assumed genotyping error rate (passed to est.map).
map.function Map function to be used (passed to est.map).

Value

The input cross object, but with the marker order on the specified chromosome updated, and with any derived data removed (except for recombination fractions, if present, which are not removed); the genetic map for the relevant chromosome is re-estimated.

Author(s)

Karl W Broman, kbroman@jhsph.edu

See Also

ripple, clean

Examples

data(fake.f2)
fake.f2 <- switch.order(fake.f2, 1, c(1,3,2,4:7))

[Package qtl version 0.98-57 Index]