compare_orders: Compare potential orders for linkage groups

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Compares potential orderings on the number of expected crossovers or likelihood values. Rewrite of older version.

Usage

compare_orders(cross, chr, orders, method = c("countXO", "likelihood"))

Arguments

cross	Object of class mpcross or cross
chr	Selected chromosomes
orders	Orders to be compared
method	Method for comparison. Note that "likelihood" is much more time-consuming than "countXO"

Details

Uses functions from R/qtl in order to compare possible orderings on the basis of the number of obligate crossovers or log-likelihood values.

Value

The matrix of orders with crossover counts appended.

References

R/qtl

See Also

mporder, countXO

Examples

map <- qtl::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)))

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.