matchGroups: Combine two cutpoint groups and pass them into LKH and return...

In mckaylab/TSPmap: A tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps

Description

Combine two cutpoint groups and pass them into LKH and return the value of the second largest rf value in the result. This is used to pair small subgroups with a larger group by combining the small group with all larger groups and seeing which results in the smallest return value. The reason we take the second largest rf value in the TSP result is because the largest rf value represents the completion of the TSP circuit, so even for a single chromosome this will be a large value.

Usage

matchGroups(ind_group1,ind_group2, markerData, cutList, rfmatrix, execPath)

Arguments

ind_group1	- index of the first group
ind_group2	- index of the second group
markerData	- main marker data file, produced by either the readfile.R/readFile function or the duplicatemarkers.R/removedups function
cutList	- cutpoint array, produced by cutpoints.R/findcuts function
rfmatrix	- recombination frequency matrix, produced by the rfmatrix.R/computeRFmat function
execPath	- path to LKH executable

Value

Maximum rf value in the TSP path of the two clusters combined.

mckaylab/TSPmap documentation built on Aug. 19, 2021, 8:38 p.m.