merge_homologues

A <code>data.frame</code> with markernames, linkage group (<code>"LG"</code>) and homologue (<code>"homologue"</code>)

LG_hom_stack

The ploidy level of the plant species.

ploidy

The linkage group where the to be merged homologue fragments are in.

A list of vectors of length 2, specifying the numbers of the homologue fragments to be merged. User input is asked if <code>NULL</code>.

mergeList

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Based on additional information, homologue fragments, separated during clustered should be merged again.
<code>merge_homologues</code> allows to merge homologues per linkage group based on user input.

Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (submitted, 2020).

Peter Bourke

polymapR

Linkage Analysis in Outcrossing Polyploids

Geert van Geest

Roeland Voorrips

Yanlin Liao

merge_homologues function

<dl><dt>LG_hom_stack</dt>
<dd>A <code>data.frame</code> with markernames, linkage group (<code>"LG"</code>) and homologue (<code>"homologue"</code>)</dd>
<dt>ploidy</dt>
<dd>The ploidy level of the plant species.</dd>
<dt>LG</dt>
<dd>The linkage group where the to be merged homologue fragments are in.</dd>
<dt>mergeList</dt>
<dd>A list of vectors of length 2, specifying the numbers of the homologue fragments to be merged. User input is asked if <code>NULL</code>.</dd>
<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.</dd></dl>

Arguments

Merge homologues — merge_homologues

<dl>

<dt>LG_hom_stack</dt>
<dd>A <code>data.frame</code> with markernames, linkage group (<code>"LG"</code>) and homologue (<code>"homologue"</code>)</dd>


<dt>ploidy</dt>
<dd>The ploidy level of the plant species.</dd>


<dt>LG</dt>
<dd>The linkage group where the to be merged homologue fragments are in.</dd>


<dt>mergeList</dt>
<dd>A list of vectors of length 2, specifying the numbers of the homologue fragments to be merged. User input is asked if <code>NULL</code>.</dd>


<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.</dd>

</dl>

merge_homologues: Merge homologues

Description

Usage

Value

Arguments

Examples