mpMap (version 1.14)

compare_orders: Compare potential orders for linkage groups

Description

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

Usage

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)

Arguments

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.

Value

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

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.

References

R/qtl

See Also

mporder, ripple

Examples

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)))