lgV.txt

<p>A dataset containing the pairwise recombinations fractions for 238 SNP markers 
from linkage group V of potato. These are derived from the genotypes of 190 
offspring from a cross between potato cultivar Stirling and the breeding line 
12601ab1. Further details are available in Hackett et al. (2013).</p>

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

lgV.txt function

<p>An ascii text file in the format described in <code>calc.maps.pc</code> 
and <code>calc.maps.sphere</code>. The first line contains the number of markers
and the number of combinations. Then follow the space-separated combinations with
their recombination fractions and LOD scores:</p>
<table class="table">
<tr><td></td><td><code>nmarkers</code></td><td></td><td></td></tr>
<tr><td></td><td><code>marker_1</code></td><td><code>marker_2</code></td><td><code>recombination fraction</code></td></tr>
<tr><td><code>LOD</code></td><td><code>1</code></td><td><code>2</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>1</code></td><td><code>3</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>1</code></td><td><code>4</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>2</code></td><td><code>3</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>2</code></td><td><code>4</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
</table><p></p><p></p>

Format

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

<p>An ascii text file in the format described in <code>calc.maps.pc</code> 
and <code>calc.maps.sphere</code>. The first line contains the number of markers
and the number of combinations. Then follow the space-separated combinations with
their recombination fractions and LOD scores:</p>
<table class='table'>
<tr><td></td><td><code>nmarkers</code></td><td></td><td></td></tr>
<tr><td></td><td><code>marker_1</code></td><td><code>marker_2</code></td><td><code>recombination fraction</code></td></tr>
<tr><td><code>LOD</code></td><td><code>1</code></td><td><code>2</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>1</code></td><td><code>3</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>1</code></td><td><code>4</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>2</code></td><td><code>3</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>2</code></td><td><code>4</code></td><td><code>.</code></td></tr>
<tr><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td><td><code>.</code></td></tr>
</table>



	`nmarkers`
	`marker_1`	`marker_2`	`recombination fraction`
`LOD`	`1`	`2`	`.`
`.`	`1`	`3`	`.`
`.`	`1`	`4`	`.`
`.`	`.`	`.`	`.`
`.`	`.`	`.`	`.`
`.`	`.`	`.`	`.`
`.`	`2`	`3`	`.`
`.`	`2`	`4`	`.`
`.`	`.`	`.`	`.`

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

Description

Arguments

Format

lgV.txt

Examples