High Density Genetic Linkage Mapping using Multidimensional Scaling
Estimate marker positions using Principal Curves
Estimate marker positions using spherically constrained weighted MDS
Nearest neighbour fit from estimated map and file of pairwise recombin...
Calculates the nearest neighbour fit for an individual marker.
Calculate the nearest neighbour fit.
Calculates the number of swaps required to move from one order to anot...
Create recombination matrix from pairwise data file.
Convert Cartesian coordinates from wMDS coordinates to polar coordinat...
Reorders a distance map by a new marker order.
Calculates pairwise map distances from the recombination fraction.
Load data, estimate a linkage map and plot diagnostics for the fit.
Calculates the distance of a marker from some objective "truth".
For a given marker finds the nearest neighbours with LOD scores > 0.
Invert the order of locimap from an estimated map.
Dataset lgI.txt: pairwise recombination fractions for 143 markers.
Dataset lgV.txt: pairwise recombination fractions for 238 markers.
Map points from MDS final configuration to interval starting at 0.
High density Genetic Linkage Mapping using Multidimensional Scaling
Calculates mean square distance between marker positions in two differ...
Diagnostic plots for the map estimation using calc.maps.pc with 2 dime...
Diagnostic plots for the map estimation using calc.maps.pc with 3 dime...
Produces diagnostic plots for the estimated map using `calc.maps.spher...
Calculate a nearest neighbour fit from an estimated map object.
Simulate a backcross population from homozygous parents.
Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.