compare_orders: Compare potential orders for linkage groups
In mpMap: Multi-parent RIL genetic analysis

Description Usage Arguments Details Value References See Also Examples

Compares potential orderings on the basis of likelihood or number of expectedcrossovers. Based off of the ripple function in R/qtl.

  compare_orders(cross, chr, orders, window = 2,
    method = c("countxo", "likelihood"),
    error.prob = 1e-04,
    map.function = c("haldane", "kosambi", "c-f", "morgan"),
    maxit = 4000, tol = 1e-06, sex.sp = TRUE,
    verbose = TRUE)

`cross`	Object of class `mpcross` or `cross`
`chr`	Selected chromosomes
`orders`	Orders to be compared
`window`	Window size for order comparison
`method`	Method for comparison, either counting the number of crossovers or likelihood value. See `ripple` for further details.
`error.prob`	See `ripple` for details.
`map.function`	See `ripple` for details.
`maxit`	See `ripple` for details.
`tol`	See `ripple` for details.
`sex.sp`	See `ripple` for details.
`verbose`	See `ripple` for details.

Uses the core of the ripple function from R/qtl in order to compare orderings output from mporder. Note that method="likelihood" is substantially slower than method="countxo" and should not be used for a large number of orderings or a large window size.

The matrix of orders with crossover counts or likelihood values appended. Similar output to ripple.

R/qtl

mporder, ripple

map <- sim.map(len=100, n.mar=11, eq.spacing=TRUE, include.x=FALSE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, seed=1)
compare_orders(sim.dat, chr=1, orders=rbind(1:11, c(1:3, 6:4, 7:11)))