tspOrder: Order markers within linkage groups

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

tspOrder Apply a traveling salesperson problem solver to find the shortest path through the recombination fraction matrix. Requires that the TSP R package and the TSP solver "Concorde" program are installed. See details.

Usage

tspOrder(cross, concorde_path, return = "cross")

Arguments

cross	The QTL cross object.
concorde_path	Required. The directory containing concorde executables.
return	If "cross" is specified, pass the marker order through newLG, which quickly reorders the markers of the original cross to follow the TSP order. Otherwise, return a named list of markers in order for each chromosome.
...	Additional arguments passed on to solve_TSP that are then paseed to TSP::contol.

Details

This function relies on the TSP R packages to perform the TSP solvers. See documentation therein, esspecially the function TSP::solve_TSP. We permit inference of marker order within a Hamiltonian circuit by adding a dummy node that has 0 distance to all other nodes. This allows for discrete start and end points and is more appropriate for genetic map construction than forcing a complete route through all markers.

To install the concorde program: http://www.math.uwaterloo.ca/tsp/concorde/downloads/codes/src/co031219.tgz. If on a mac, this is not super easy. See https://qmha.wordpress.com/2015/08/20/installing-concorde-on-mac-os-x/ for details on the best way to do this.

Value

Either a cross object with reordered markers, or a named list of markers in a new order.

Examples

## Not run: 
library(qtlTools)
set.seed(42)
map<-sim.map(len = 200, n.mar = 200, include.x = F, eq.spacing=T)
cross<-sim.cross(map, type = "riself", map.function = "kosambi", error.prob = 0)
cross<-est.rf(cross)
markerlist<-lapply(chrnames(cross), function(x) sample(markernames(cross, chr =x)))
names(markerlist)<-as.character(chrnames(cross))
cross.rand<-newLG(cross, markerList = markerlist)
set.seed(42)
cross.ord<-tspOrder(cross = cross.rand,
  max.rf = .5,
  concorde_path = "/Users/John/Documents/concorde/TSP")

plot(match(markernames(cross), markernames(cross.ord)),
xlab = "position in similated map", ylab = "position in ordered map")

## End(Not run)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.