define_LG_structure

Function which organises the output of <code>cluster_SN_markers</code> into a data frame of numbered linkage groups and homologues.
Only use this function if it is clear from the graphical output of <code>cluster_SN_markers</code> that there are LOD scores present which define both chromosomes (lower LOD)
and homologues (higher LOD).

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. (2021) <doi:10.1007/s00122-021-03834-x>.

Peter Bourke

polymapR

Linkage Analysis in Outcrossing Polyploids

Geert van Geest

Roeland Voorrips

Yanlin Liao

define_LG_structure function

<dl><dt>cluster_list</dt>
<dd>A list of cluster_stacks, the output of <code>cluster_SN_markers</code>.</dd>
<dt>LOD_chm</dt>
<dd>Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups</dd>
<dt>LOD_hom</dt>
<dd>Integer. The LOD threshold specifying at which LOD score the markers divide into homologue groups</dd>
<dt>LG_number</dt>
<dd>Integer. Expected number of chromosomes (linkage groups). Note that if this number of clusters are not
present at LOD_chm, the function will abort.</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

Generate linkage group and homologue structure of SxN markers — define_LG_structure

<dl>

<dt>cluster_list</dt>
<dd>A list of cluster_stacks, the output of <code>cluster_SN_markers</code>.</dd>


<dt>LOD_chm</dt>
<dd>Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups</dd>


<dt>LOD_hom</dt>
<dd>Integer. The LOD threshold specifying at which LOD score the markers divide into homologue groups</dd>


<dt>LG_number</dt>
<dd>Integer. Expected number of chromosomes (linkage groups). Note that if this number of clusters are not
present at LOD_chm, the function will abort.</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>

define_LG_structure: Generate linkage group and homologue structure of SxN markers

Description

Usage

Value

Arguments

Examples