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MDSMap (version 1.3)

High Density Genetic Linkage Mapping using Multidimensional Scaling

Description

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) .

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Version

Install

install.packages('MDSMap')

Monthly Downloads

409

Version

1.3

License

GPL-3 | file LICENSE

Maintainer

Bram Boskamp

Last Published

April 28th, 2025

Functions in MDSMap (1.3)

get.nearest.informative

For a given marker finds the nearest neighbours with LOD scores > 0.
map.to.interval

Map points from MDS final configuration to interval starting at 0.
lgV.txt

Dataset lgV.txt: pairwise recombination fractions for 238 markers.
get.dist.loci

Calculates the distance of a marker from some objective "truth".
plot.pcmap

Diagnostic plots for the map estimation using calc.maps.pc with 2 dimensions.
dmap.check

Reorders a distance map by a new marker order.
meandist.from.truth

Calculates mean square distance between marker positions in two different maps.
invert.map

Invert the order of locimap from an estimated map.
estimate.map

Load data, estimate a linkage map and plot diagnostics for the fit.
lgI.txt

Dataset lgI.txt: pairwise recombination fractions for 143 markers.
plot.pcmap3d

Diagnostic plots for the map estimation using calc.maps.pc with 3 dimensions.
recalc.nnfit.from.map

Calculate a nearest neighbour fit from an estimated map object.
plot.spheremap

Produces diagnostic plots for the estimated map using calc.maps.sphere.
sim.bc.rflod.file

Simulate a backcross population from homozygous parents.
calc.nnfit.from.file

Nearest neighbour fit from estimated map and file of pairwise recombination fractions.
calc.maps.sphere

Estimate marker positions using spherically constrained weighted MDS
calc.pair.rf.lod

Create recombination matrix from pairwise data file.
calc.nnfit.loci

Calculates the nearest neighbour fit for an individual marker.
MDSMap-package

High density Genetic Linkage Mapping using Multidimensional Scaling
calc.nnfit

Calculate the nearest neighbour fit.
convert.polar

Convert Cartesian coordinates from wMDS coordinates to polar coordinates.
dmap

Calculates pairwise map distances from the recombination fraction.
calc.maps.pc

Estimate marker positions using Principal Curves
calc.nswaps

Calculates the number of swaps required to move from one order to another.