autoClusterMST: Break the markers into clusters.

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

split the MST into a number of clusters equal to 1.5 times the number of chromosomes. A cluster, in this case, must be at least numMarkers/(2*numChromosomes) in size, so that we don't count exceedingly small groups toward the total number.

Usage

autoClusterMST(rawdata, rfmat, numChromosomes,
LKHexec, internalRfThreshold)

Arguments

rawdata	- raw marker data
rfmat	- recombination frequency matrix, produced by the rfmatrix.R/computeRFmat function
numChromosomes	- number of chromosomes
LKHexec	- path and filename of LKH executable - must not contain the tilde character!
internalRfThreshold	- if a cluster contains an rf value this large, it probably contains markers from two different chromosomes. The clusters will be split until no rf values exceeding this threshold exist within any cluster.

Value

Returns the list of clusters of marker IDs.

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