Learn R Programming

⚠️There's a newer version (1.3) of this package.Take me there.

MDSMap (version 1.1)

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) .

Copy Link

Version

Install

install.packages('MDSMap')

Monthly Downloads

349

Version

1.1

License

GPL-3 | file LICENSE

Maintainer

Bram Boskamp

Last Published

August 9th, 2018

Functions in MDSMap (1.1)

meandist.from.truth

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

Dataset lgV.txt: pairwise recombination fractions for 238 markers.

map.to.interval

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

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

calc.maps.sphere

Estimate marker positions using spherically constrained weighted MDS

Reorders a distance map by a new marker order.

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

calc.nnfit.from.file

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

Produces diagnostic plots for the estimated map using calc.maps.sphere.

Calculate the nearest neighbour fit.

Invert the order of locimap from an estimated map.

calc.nnfit.loci

Calculates the nearest neighbour fit for an individual marker.

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

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.

Convert Cartesian coordinates from wMDS coordinates to polar coordinates.

Calculates pairwise map distances from the recombination fraction.

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.

Estimate marker positions using Principal Curves

High density Genetic Linkage Mapping using Multidimensional Scaling

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

calc.pair.rf.lod

Create recombination matrix from pairwise data file.

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