MDSMap-package          High density Genetic Linkage Mapping using
                        Multidimensional Scaling
calc.maps.pc            Estimate marker positions using Principal
                        Curves
calc.maps.sphere        Estimate marker positions using spherically
                        constrained weighted MDS
calc.nnfit              Calculate the nearest neighbour fit.
calc.nnfit.from.file    Nearest neighbour fit from estimated map and
                        file of pairwise recombination fractions.
calc.nnfit.loci         Calculates the nearest neighbour fit for an
                        individual marker.
calc.nswaps             Calculates the number of swaps required to move
                        from one order to another.
calc.pair.rf.lod        Create recombination matrix from pairwise data
                        file.
convert.polar           Convert Cartesian coordinates from wMDS
                        coordinates to polar coordinates.
dmap                    Calculates pairwise map distances from the
                        recombination fraction.
dmap.check              Reorders a distance map by a new marker order.
estimate.map            Load data, estimate a linkage map and plot
                        diagnostics for the fit.
get.dist.loci           Calculates the distance of a marker from some
                        objective "truth".
get.nearest.informative
                        For a given marker finds the nearest neighbours
                        with LOD scores > 0.
invert.map              Invert the order of locimap from an estimated
                        map.
lgI.txt                 Dataset lgI.txt: pairwise recombination
                        fractions for 143 markers.
lgV.txt                 Dataset lgV.txt: pairwise recombination
                        fractions for 238 markers.
map.to.interval         Map points from MDS final configuration to
                        interval starting at 0.
meandist.from.truth     Calculates mean square distance between marker
                        positions in two different maps.
plot.pcmap              Diagnostic plots for the map estimation using
                        calc.maps.pc with 2 dimensions.
plot.pcmap3d            Diagnostic plots for the map estimation using
                        calc.maps.pc with 3 dimensions.
plot.spheremap          Produces diagnostic plots for the estimated map
                        using 'calc.maps.sphere'.
recalc.nnfit.from.map   Calculate a nearest neighbour fit from an
                        estimated map object.
sim.bc.rflod.file       Simulate a backcross population from homozygous
                        parents.
