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
| 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. |
