addMarkerNames | add marker names |
addRfs | Internal function to add rf and cumulative rf values to a... |
addStampToFilename | Add datestamp to file |
autoClusterMST | Break the markers into clusters. |
autoMergeClusters | Merge the clusters from autoClusterMST into full linkage... |
callConcorde | Run Concorde TSP solver. |
callLKH | Run LKH TSP solver. |
capRFmat | Cap the rf matrix according to the given threshold. |
checkNongroupEdges | Find the smallest edge weight between the target cluster and... |
cleanrfmat | Clean up rfmat object |
computeHaldane | Compute genetic distances (in centiMorgans) by the Haldane... |
computeKosambi | Compute genetic distances (in centiMorgans) by the Kosambi... |
computeRFmat | This function computes the recombination frequency matrix. |
createMap | Process a linkage group with Concorde to get the final... |
createMST | Create minimum spanning tree. |
createTSPFile | Create TSP problem file. |
distancedf2table | create table of marker distances and groups |
findcuts | Determine cutpoints in TSP solution object. |
finddups | This function finds duplicate markers in the main marker data... |
findZeroes | Identify redundant markers in the solution object that have... |
matchGroups | Combine two cutpoint groups and pass them into LKH and return... |
matchGroups2 | This is an alternate version of the matchGroups function... |
MSTcallTSP | Call the LKH solver and process the results. |
MSTgetGroup | Get the marker IDs for a particular cluster |
pareMatrix | This function pares down a given rf matrix by keeping or... |
plotTSPsoln | Plot the TSP solution |
processConcordeOutput | Process Concorde solution file |
processLKHOutput | Process LKH solution file. |
readFile | This function reads in a raw data file from disk. |
rearrangeGroup | Merge two clusters. |
removedups | This function removes duplicate markers from the main marker... |
removeMarkers | Remove redundant markers. |
reorderMarkers | Reorder raw marker data |
reverseCluster | Reverse the order of markers in a group within a cluster. |
reverseGroup | Reverse the order of markers in a group within a TSP solution... |
selectGroup | Return the list of marker indices that comprise the given... |
shiftTSPsoln | Shift a TSP solution array when the endpoints don't line up... |
sortRFmatrix | This function sorts the rfmatrix so that the markers are in... |
TSPmap2distancedf | convert final tspmap to distance data.frame |
tspOrder | Order markers within linkage groups |
writeOutput | Write the TSP solution object to a comma-separated value... |
writeRFmat | writes the recombination frequency matrix to a file |
writeSortedRFmat | Write the sorted RF matrix to file. |
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