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

addMarkerNamesadd marker names
addRfsInternal function to add rf and cumulative rf values to a...
addStampToFilenameAdd datestamp to file
autoClusterMSTBreak the markers into clusters.
autoMergeClustersMerge the clusters from autoClusterMST into full linkage...
callConcordeRun Concorde TSP solver.
callLKHRun LKH TSP solver.
capRFmatCap the rf matrix according to the given threshold.
checkNongroupEdgesFind the smallest edge weight between the target cluster and...
cleanrfmatClean up rfmat object
computeHaldaneCompute genetic distances (in centiMorgans) by the Haldane...
computeKosambiCompute genetic distances (in centiMorgans) by the Kosambi...
computeRFmatThis function computes the recombination frequency matrix.
createMapProcess a linkage group with Concorde to get the final...
createMSTCreate minimum spanning tree.
createTSPFileCreate TSP problem file.
distancedf2tablecreate table of marker distances and groups
findcutsDetermine cutpoints in TSP solution object.
finddupsThis function finds duplicate markers in the main marker data...
findZeroesIdentify redundant markers in the solution object that have...
matchGroupsCombine two cutpoint groups and pass them into LKH and return...
matchGroups2This is an alternate version of the matchGroups function...
MSTcallTSPCall the LKH solver and process the results.
MSTgetGroupGet the marker IDs for a particular cluster
pareMatrixThis function pares down a given rf matrix by keeping or...
plotTSPsolnPlot the TSP solution
processConcordeOutputProcess Concorde solution file
processLKHOutputProcess LKH solution file.
readFileThis function reads in a raw data file from disk.
rearrangeGroupMerge two clusters.
removedupsThis function removes duplicate markers from the main marker...
removeMarkersRemove redundant markers.
reorderMarkersReorder raw marker data
reverseClusterReverse the order of markers in a group within a cluster.
reverseGroupReverse the order of markers in a group within a TSP solution...
selectGroupReturn the list of marker indices that comprise the given...
shiftTSPsolnShift a TSP solution array when the endpoints don't line up...
sortRFmatrixThis function sorts the rfmatrix so that the markers are in...
TSPmap2distancedfconvert final tspmap to distance data.frame
tspOrderOrder markers within linkage groups
writeOutputWrite the TSP solution object to a comma-separated value...
writeRFmatwrites the recombination frequency matrix to a file
writeSortedRFmatWrite the sorted RF matrix to file.
mckaylab/TSPmap documentation built on Oct. 19, 2018, 5:26 a.m.