recalc.nnfit.from.map

Calculates a new nearest neighbour fit based on a new order from a map object 
generated by <code>calc.maps.pc</code>, <code>calc.maps.sphere</code> or 
<code>estimate.map</code>

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) <doi:10.1007/s00122-016-2761-8>.

Bram Boskamp

MDSMap

High Density Genetic Linkage Mapping using Multidimensional
Scaling

recalc.nnfit.from.map function

<dl><dt>estmap</dt>
<dd>A character string indicating the name of a comma separated value 
file with the first column containing marker names in the order of their estimated position.</dd>
<dt>mapobject</dt>
<dd>A map object generated by <code>calc.maps.pc</code>, 
<code>calc.maps.sphere</code> or <code>estimate.map</code>.</dd>
<dt>header</dt>
<dd>Logical argument indicating whether the .csv file <code>estmap</code> 
contains headers - default is <code>TRUE</code></dd></dl>

Arguments

Calculate a nearest neighbour fit from an estimated map object. — recalc.nnfit.from.map

<dl>

<dt>estmap</dt>
<dd>A character string indicating the name of a comma separated value 
file with the first column containing marker names in the order of their estimated position.</dd>


<dt>mapobject</dt>
<dd>A map object generated by <code>calc.maps.pc</code>, 
<code>calc.maps.sphere</code> or <code>estimate.map</code>.</dd>


<dt>header</dt>
<dd>Logical argument indicating whether the .csv file <code>estmap</code> 
contains headers - default is <code>TRUE</code></dd>

</dl>

recalc.nnfit.from.map: Calculate a nearest neighbour fit from an estimated map object.

Description

Usage

Value

Arguments

Details

See Also