autoMergeClusters: Merge the clusters from autoClusterMST into full linkage...
In mckaylab/TSPmap: A tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps

Starting with the clusters produced by autoClusterMST, this function merges them until we are left with full linkage groups.

1 2	autoMergeClusters(clusterlist, rfmat, LKHexec, numChromosomes, rfCap = 0, minMergeWeight = 0.40, rawdata)

`clusterlist`	- list of clusters produced by autoClusterMST
`rfmat`	- recombination frequency matrix, produced by the rfmatrix.R/computeRFmat function
`LKHexec`	- path and filename of LKH executable - must not contain the tilde character!
`numChromosomes`	- number of chromosomes
`rfCap`	- value at which the rf matrix was capped.
`minMergeWeight`	- this is the minimum weight that will cause two clusters to be merged. If the min weight between the two groups exceeds this threshold, the two groups will not be merged.
`rawdata`	original raw marker data that was read into the R session

Returns the list of linkage groups.

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

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