High Density Genetic Linkage Mapping using Multidimensional Scaling

Documentation for package ‘MDSMap’ version 1.1

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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.