R: High Density Genetic Linkage Mapping using Multidimensional Scaling

# High Density Genetic Linkage Mapping using Multidimensional Scaling

## Documentation for package ‘MDSMap’ version 1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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.