switch.order: 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)
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 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.
Value
The input cross object, but with the marker order on the
specified chromosome updated.
The output object is "cleaned" of any intermediate calculations (such
as from calc.genoprob, because these values have no
meaning with a change in marker order.
We re-estimate the genetic map for the relevant chromosome.